Tried to make the fusion with Aidan Thomps modification of compute_born + several headers issues (essentially adding override flag to virtual methods)
This commit is contained in:
Germain Clavier
@ -129,6 +129,7 @@ OPT.
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* :doc:`npt/sphere (o) <fix_npt_sphere>`
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* :doc:`npt/uef <fix_nh_uef>`
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* :doc:`numdiff <fix_numdiff>`
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* :doc:`numdiff/virial <fix_numdiff_virial>`
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* :doc:`nve (giko) <fix_nve>`
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* :doc:`nve/asphere (gi) <fix_nve_asphere>`
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* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
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@ -225,7 +225,7 @@ follows:
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commands in an input script.
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- The Force class computes various forces between atoms. The Pair
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parent class is for non-bonded or pair-wise forces, which in LAMMPS
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parent class is for non-bonded or pairwise forces, which in LAMMPS
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also includes many-body forces such as the Tersoff 3-body potential if
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those are computed by walking pairwise neighbor lists. The Bond,
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Angle, Dihedral, Improper parent classes are styles for bonded
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@ -1941,6 +1941,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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*Compute ID for fix numdiff does not exist*
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Self-explanatory.
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*Compute ID for fix numdiff/virial does not exist*
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Self-explanatory.
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*Compute ID for fix store/state does not exist*
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Self-explanatory.
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@ -3796,6 +3799,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
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Self-explanatory. Efficient loop over all atoms for numerical
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difference requires consecutive atom IDs.
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*Fix numdiff/virial must use group all*
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Virial contributions computed by this fix are
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computed on all atoms.
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*Fix nve/asphere requires extended particles*
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This fix can only be used for particles with a shape setting.
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@ -416,7 +416,7 @@ This will most likely cause errors in kinetic fluctuations.
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not defined for the specified atom style.
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*Molecule has bond topology but no special bond settings*
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This means the bonded atoms will not be excluded in pair-wise
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This means the bonded atoms will not be excluded in pairwise
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interactions.
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*Molecule template for create_atoms has multiple molecules*
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@ -305,6 +305,40 @@ you are uncertain, please ask.
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FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg`
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convenience function where possible.
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- Usage of C++11 `virtual`, `override`, `final` keywords: Please follow the
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`C++ Core Guideline C.128 <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Rh-override>`_.
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That means, you should only use `virtual` to declare a new virtual
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function, `override` to indicate you are overriding an existing virtual
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function, and `final` to prevent any further overriding.
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- Trivial destructors: Prefer not writing destructors when they are empty and `default`.
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.. code-block:: c++
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// don't write destructors for A or B like this
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class A : protected Pointers {
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public:
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A();
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~A() override {}
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};
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class B : protected Pointers {
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public:
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B();
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~B() override = default;
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};
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// instead, let the compiler create the implicit default destructor by not writing it
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class A : protected Pointers {
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public:
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A();
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};
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class B : protected Pointers {
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public:
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B();
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};
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- Header files, especially those defining a "style", should only use
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the absolute minimum number of include files and **must not** contain
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any ``using`` statements. Typically that would be only the header for
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@ -106,7 +106,7 @@ individual ranks. Here is an example output for this section:
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----------
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The third section above lists the number of owned atoms (Nlocal),
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ghost atoms (Nghost), and pair-wise neighbors stored per processor.
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ghost atoms (Nghost), and pairwise neighbors stored per processor.
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The max and min values give the spread of these values across
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processors with a 10-bin histogram showing the distribution. The total
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number of histogram counts is equal to the number of processors.
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@ -114,7 +114,7 @@ number of histogram counts is equal to the number of processors.
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----------
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The last section gives aggregate statistics (across all processors)
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for pair-wise neighbors and special neighbors that LAMMPS keeps track
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for pairwise neighbors and special neighbors that LAMMPS keeps track
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of (see the :doc:`special_bonds <special_bonds>` command). The number
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of times neighbor lists were rebuilt is tallied, as is the number of
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potentially *dangerous* rebuilds. If atom movement triggered neighbor
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@ -214,7 +214,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
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The default for the :doc:`package kokkos <package>` command when
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running on KNL is to use "half" neighbor lists and set the Newton flag
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to "on" for both pairwise and bonded interactions. This will typically
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be best for many-body potentials. For simpler pair-wise potentials, it
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be best for many-body potentials. For simpler pairwise potentials, it
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may be faster to use a "full" neighbor list with Newton flag to "off".
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Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
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the default :doc:`package kokkos <package>` options. See its page for
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@ -383,7 +383,7 @@ multiple groups, its weight is the product of the weight factors.
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This weight style is useful in combination with pair style
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:doc:`hybrid <pair_hybrid>`, e.g. when combining a more costly many-body
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potential with a fast pair-wise potential. It is also useful when
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potential with a fast pairwise potential. It is also useful when
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using :doc:`run_style respa <run_style>` where some portions of the
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system have many bonded interactions and others none. It assumes that
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the computational cost for each group remains constant over time.
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@ -8,10 +8,19 @@ Syntax
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.. parsed-literal::
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compute ID group-ID born/matrix
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compute ID group-ID born/matrix keyword value ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* born/matrix = style name of this compute command
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* one or more keyword/value pairs may be appended
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.. parsed-literal::
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*numdiff* values = delta virial-ID
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delta = magnitude of strain fields (dimensionless)
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virial-ID = ID of pressure compute for virial (string)
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*pair* or *bond* or *angle* or *dihedral* values = none
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Examples
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""""""""
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@ -19,6 +28,8 @@ Examples
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.. code-block:: LAMMPS
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compute 1 all born/matrix
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compute 1 all born/matrix bond angle
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compute 1 all born/matrix numdiff 1.0e-4 myvirial
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Description
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"""""""""""
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@ -33,7 +44,7 @@ tensor :math:`\varepsilon` elements. These values are related to:
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C^{B}_{i,j}=\frac{1}{V}\frac{\partial{}^2U}{\partial{}\varepsilon_{i}\partial\varepsilon_{j}}
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also called the Born term of elastic constants in the stress-stress fluctuation
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formalism. This quantity can be used to compute the elastic constant tensor.
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formalism. This quantity can be used to compute the elastic constant tensor.
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Using the symmetric Voigt notation, the elastic constant tensor can be written
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as a 6x6 symmetric matrix:
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@ -96,6 +107,58 @@ solid the virial stress can have large variations between timesteps and average
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values can be slow to converge. This term is better computed using
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instantaneous values.
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Two different computation methods are implemented in this compute and are
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mutually exclusive.
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The first one is a direct computation from the analytical formula from the
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different terms of the potential used for the simulations (see :ref: `(Vorkum)
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<_VanWorkum>`). However, the implementation of such derivations must be done
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for every potential form. This has not been done yet and can be very
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complicated for sophisticated potentials. At the moment a warning message is
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displayed for every term that is not supporting the compute at the moment.
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This method is the default for now.
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The second method uses finite differences of energy to numerically approximate
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the second derivatives (see :ref: `(Zhen) <_Zhen>`). This is useful when using
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interaction styles for which the analytical second derivatives have not been
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implemented. In this cases, the compute applies linear strain fields of
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magnitude *delta* to all the atoms relative to a point at the center of the
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box. The strain fields are in six different directions, corresponding to the
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six Cartesian components of the stress tensor defined by LAMMPS. For each
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direction it applies the strain field in both the positive and negative senses,
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and the new stress virial tensor of the entire system is calculated after each.
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The difference in these two virials divided by two times *delta*, approximates
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the corresponding components of the second derivative, after applying a
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suitable unit conversion.
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.. note::
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It is important to choose a suitable value for delta, the magnitude of
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strains that are used to generate finite difference
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approximations to the exact virial stress. For typical systems, a value in
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the range of 1 part in 1e5 to 1e6 will be sufficient.
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However, the best value will depend on a multitude of factors
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including the stiffness of the interatomic potential, the thermodynamic
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state of the material being probed, and so on. The only way to be sure
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that you have made a good choice is to do a sensitivity study on a
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representative atomic configuration, sweeping over a wide range of
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values of delta. If delta is too small, the output values will vary
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erratically due to truncation effects. If delta is increased beyond a
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certain point, the output values will start to vary smoothly with
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delta, due to growing contributions from higher order derivatives. In
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between these two limits, the numerical virial values should be largely
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independent of delta.
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The keyword requires the additional arguments *delta* and *virial-ID*.
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*delta* gives the size of the applied strains. *virial-ID* gives
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the ID string of the pressure compute that provides the virial stress tensor,
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requiring that it use the virial keyword e.g.
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.. code-block:: LAMMPS
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compute myvirial all pressure NULL virial
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compute 1 all born/matrix numdiff 1.0e-4 myvirial
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**Output info:**
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This compute calculates a global array with the number of rows=21.
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@ -110,15 +173,18 @@ Restrictions
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""""""""""""
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This compute is part of the EXTRA-COMPUTE package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info. LAMMPS was built with that package. See
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the :doc:`Build package <Build_package>` page for more info.
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The Born term can be decomposed as a product of two terms. The first one
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is a general term which depends on the configuration. The second one is
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specific to every interaction composing your force field (non-bonded,
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bonds, angle...). Currently not all interaction implement the *born_matrix*
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method giving first and second order derivatives and a warning will
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be raised if you try to use this compute with such interactions. The returned
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values of this force field component is currently zero.
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The Born term can be decomposed as a product of two terms. The first one is a
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general term which depends on the configuration. The second one is specific to
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every interaction composing your force field (non-bonded, bonds, angle...).
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Currently not all LAMMPS interaction styles implement the *born_matrix* method
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giving first and second order derivatives and LAMMPS will exit with an error if
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this compute is used with such interactions unless the *numdiff* option is
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also used. The *numdiff* option cannot be used with any other keyword. In this
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situation, LAMMPS will also exit with an error.
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Default
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"""""""
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@ -134,3 +200,7 @@ none
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.. _Voyiatzis:
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**(Voyiatzis)** E. Voyiatzis, Computer Physics Communications 184(2013)27-33
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.. _Zhen:
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**(Zhen)** Y. Zhen, C. Chu, Computer Physics Communications 183(2012)261-265
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@ -141,7 +141,7 @@ Related commands
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""""""""""""""""
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:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
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:doc:`thermo_style <thermo_style>`,
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:doc:`thermo_style <thermo_style>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
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Default
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"""""""
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@ -61,7 +61,7 @@ Restrictions
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This compute currently calculates the pressure tensor contributions
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for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
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and in the presence of bonded interactions, the result will be incorrect
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due to exclusions for special bonds) and requires pair-wise force
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due to exclusions for special bonds) and requires pairwise force
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calculations not available for most many-body pair styles. K-space
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calculations are also excluded. Note that this pressure compute outputs
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the configurational terms only; the kinetic contribution is not included
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@ -17,13 +17,14 @@ Syntax
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* one or more keyword/value pairs may be appended
|
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|
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* these keywords apply to various dump styles
|
||||
* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
|
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* keyword = *append* or *at* or *balance* or *buffer* or *delay* or *element* or *every* or *every/time* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap*
|
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|
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.. parsed-literal::
|
||||
|
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*append* arg = *yes* or *no*
|
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*at* arg = N
|
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N = index of frame written upon first dump
|
||||
*balance* arg = *yes* or *no*
|
||||
*buffer* arg = *yes* or *no*
|
||||
*delay* arg = Dstep
|
||||
Dstep = delay output until this timestep
|
||||
@ -667,6 +668,14 @@ keywords are set to non-default values (i.e. the number of dump file
|
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pieces is not equal to the number of procs), then sorting cannot be
|
||||
performed.
|
||||
|
||||
In a parallel run, the per-processor dump file pieces can have
|
||||
significant imbalance in number of lines of per-atom info. The *balance*
|
||||
keyword determines whether the number of lines in each processor
|
||||
snapshot are balanced to be nearly the same. A balance value of *no*
|
||||
means no balancing will be done, while *yes* means balancing will be
|
||||
performed. This balancing preserves dump sorting order. For a serial
|
||||
run, this option is ignored since the output is already balanced.
|
||||
|
||||
.. note::
|
||||
|
||||
Unless it is required by the dump style, sorting dump file
|
||||
@ -832,6 +841,7 @@ Default
|
||||
The option defaults are
|
||||
|
||||
* append = no
|
||||
* balance = no
|
||||
* buffer = yes for dump styles *atom*, *custom*, *loca*, and *xyz*
|
||||
* element = "C" for every atom type
|
||||
* every = whatever it was set to via the :doc:`dump <dump>` command
|
||||
|
||||
@ -271,7 +271,8 @@ accelerated styles exist.
|
||||
* :doc:`npt/eff <fix_nh_eff>` - NPT for nuclei and electrons in the electron force field model
|
||||
* :doc:`npt/sphere <fix_npt_sphere>` - NPT for spherical particles
|
||||
* :doc:`npt/uef <fix_nh_uef>` - NPT style time integration with diagonal flow
|
||||
* :doc:`numdiff <fix_numdiff>` - compute derivatives of per-atom data from finite differences
|
||||
* :doc:`numdiff <fix_numdiff>` - numerically approximate atomic forces using finite energy differences
|
||||
* :doc:`numdiff/virial <fix_numdiff_virial>` - numerically approximate virial stress tensor using finite energy differences
|
||||
* :doc:`nve <fix_nve>` - constant NVE time integration
|
||||
* :doc:`nve/asphere <fix_nve_asphere>` - NVE for aspherical particles
|
||||
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>` - NVE for aspherical particles without forces
|
||||
|
||||
@ -20,13 +20,13 @@ Syntax
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
|
||||
keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *rxd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
|
||||
*pH* value = pH of the solution (can be specified as an equal-style variable)
|
||||
*pKa* value = acid dissociation constant
|
||||
*pKb* value = base dissociation constant
|
||||
*pIp* value = chemical potential of free cations
|
||||
*pIm* value = chemical potential of free anions
|
||||
*pKs* value = solution self-dissociation constant
|
||||
*pKa* value = acid dissociation constant (in the -log10 representation)
|
||||
*pKb* value = base dissociation constant (in the -log10 representation)
|
||||
*pIp* value = activity (effective concentration) of free cations (in the -log10 representation)
|
||||
*pIm* value = activity (effective concentration) of free anions (in the -log10 representation)
|
||||
*pKs* value = solvent self-dissociation constant (in the -log10 representation)
|
||||
*acid_type* = atom type of acid groups
|
||||
*base_type* = atom type of base groups
|
||||
*lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
|
||||
@ -34,7 +34,7 @@ Syntax
|
||||
*tempfixid* value = fix ID of temperature thermostat
|
||||
*nevery* value = invoke this fix every nevery steps
|
||||
*nmc* value = number of charge regulation MC moves to attempt every nevery steps
|
||||
*xrd* value = cutoff distance for acid/base reaction
|
||||
*rxd* value = cutoff distance for acid/base reaction
|
||||
*seed* value = random # seed (positive integer)
|
||||
*tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
|
||||
*group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
|
||||
@ -47,7 +47,7 @@ Examples
|
||||
""""""""
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
|
||||
fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5.0 pKb 6.0 pH 7.0 pIp 3.0 pIm 3.0 nevery 200 nmc 200 seed 123 tempfixid fT
|
||||
|
||||
fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
|
||||
|
||||
@ -92,7 +92,11 @@ where the fix attempts to charge :math:`\mathrm{A}` (discharge
|
||||
:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
|
||||
insert (delete) a proton (atom type 2). Besides, the fix implements
|
||||
self-ionization reaction of water :math:`\emptyset \rightleftharpoons
|
||||
\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly
|
||||
\mathrm{H}^++\mathrm{OH}^-`.
|
||||
|
||||
|
||||
|
||||
However, this approach is highly
|
||||
inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
|
||||
both protons and hydroxyl ions is low, resulting in a relatively low
|
||||
acceptance rate of MC moves.
|
||||
@ -102,24 +106,31 @@ reactions, which can be easily achieved via
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
|
||||
fix acid_reaction2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
|
||||
|
||||
where particles of atom type 4 and 5 are the salt cations and anions,
|
||||
both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
|
||||
where particles of atom type 4 and 5 are the salt cations and anions, both at activity (effective concentration) of :math:`10^{-2}` mol/l, see :ref:`(Curk1) <Curk1>` and
|
||||
:ref:`(Landsgesell) <Landsgesell>` for more details.
|
||||
|
||||
|
||||
Similarly, we could have simultaneously added a base ionization reaction
|
||||
(:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
|
||||
We could have simultaneously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
|
||||
fix acid_base_reaction all charge/regulation 2 3 acid_type 1 base_type 6 pH 7.0 pKa 5.0 pKb 6.0 pIp 7.0 pIm 7.0
|
||||
|
||||
where the fix will attempt to charge :math:`\mathrm{B}` (discharge
|
||||
:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
|
||||
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If
|
||||
neither the acid or the base type is specified, for example,
|
||||
insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.
|
||||
|
||||
|
||||
Dissociated ions and salt ions can be combined into a single particle type, which reduces the number of necessary MC moves and increases sampling performance, see :ref:`(Curk1) <Curk1>`. The :math:`\mathrm{H}^+` and monovalent salt cation (:math:`\mathrm{S}^+`) are combined into a single particle type, :math:`\mathrm{X}^+ = \{\mathrm{H}^+, \mathrm{S}^+\}`. In this case "pIp" refers to the effective concentration of the combined cation type :math:`\mathrm{X}^+` and its value is determined by :math:`10^{-\mathrm{pIp}} = 10^{-\mathrm{pH}} + 10^{-\mathrm{pSp}}`, where :math:`10^{-\mathrm{pSp}}` is the effective concentration of salt cations. For example, at pH=7 and pSp=6 we would find pIp~5.958 and the command that performs reactions with combined ions could read,
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix acid_reaction_combined all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 5.958 pIm 5.958
|
||||
|
||||
|
||||
|
||||
If neither the acid or the base type is specified, for example,
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
@ -127,11 +138,11 @@ neither the acid or the base type is specified, for example,
|
||||
|
||||
the fix simply inserts or deletes an ion pair of a free cation (atom
|
||||
type 4) and a free anion (atom type 5) as done in a conventional
|
||||
grand-canonical MC simulation.
|
||||
grand-canonical MC simulation. Multivalent ions can be inserted (deleted) by using the *onlysalt* keyword.
|
||||
|
||||
|
||||
The fix is compatible with LAMMPS sub-packages such as *molecule* or
|
||||
*rigid*. That said, the acid and base particles can be part of larger
|
||||
*rigid*. The acid and base particles can be part of larger
|
||||
molecules or rigid bodies. Free ions that are inserted to or deleted
|
||||
from the system must be defined as single particles (no bonded
|
||||
interactions allowed) and cannot be part of larger molecules or rigid
|
||||
@ -153,14 +164,14 @@ Langevin thermostat:
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
The chemical potential units (e.g. pH) are in the standard log10
|
||||
The units of pH, pKa, pKb, pIp, pIm are considered to be in the standard -log10
|
||||
representation assuming reference concentration :math:`\rho_0 =
|
||||
\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit
|
||||
conversion, the length (in nanometers) of the LAMMPS unit length must be
|
||||
specified via *lunit_nm* (default is set to the Bjerrum length in water
|
||||
at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
|
||||
ideal solution limit, the concentration of free ions will be
|
||||
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
|
||||
\mathrm{mol}/\mathrm{l}`. For example, in the dilute
|
||||
ideal solution limit, the concentration of free cations will be
|
||||
:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. To perform the internal unit
|
||||
conversion, the the value of the LAMMPS unit length must be
|
||||
specified in nanometers via *lunit_nm*. The default value is set to the Bjerrum length in water
|
||||
at room temperature (0.71 nm), *lunit_nm* = 0.71.
|
||||
|
||||
The temperature used in MC acceptance probability is set by *temp*. This
|
||||
temperature should be the same as the temperature set by the molecular
|
||||
@ -171,10 +182,10 @@ thermostat fix-ID is *fT*. The inserted particles attain a random
|
||||
velocity corresponding to the specified temperature. Using *tempfixid*
|
||||
overrides any fixed temperature set by *temp*.
|
||||
|
||||
The *xrd* keyword can be used to restrict the inserted/deleted
|
||||
The *rxd* keyword can be used to restrict the inserted/deleted
|
||||
counterions to a specific radial distance from an acid or base particle
|
||||
that is currently participating in a reaction. This can be used to
|
||||
simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
|
||||
simulate more realist reaction dynamics. If *rxd* = 0 or *rxd* > *L* /
|
||||
2, where *L* is the smallest box dimension, the radial restriction is
|
||||
automatically turned off and free ion can be inserted or deleted
|
||||
anywhere in the simulation box.
|
||||
@ -258,18 +269,18 @@ Default
|
||||
|
||||
pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
|
||||
acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
|
||||
100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
|
||||
100; nmc = 100; rxd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
|
||||
[1/3, 1/3, 1/3], group-ID = all
|
||||
|
||||
----------
|
||||
|
||||
.. _Curk1:
|
||||
|
||||
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
|
||||
**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Accelerated simulation method for charge regulation effects", JCP 156 (2022).
|
||||
|
||||
.. _Curk2:
|
||||
|
||||
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
|
||||
**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL 126 (2021)
|
||||
|
||||
.. _Landsgesell:
|
||||
|
||||
|
||||
@ -13,16 +13,15 @@ Syntax
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* numdiff = style name of this fix command
|
||||
* Nevery = calculate force by finite difference every this many timesteps
|
||||
* delta = finite difference displacement length (distance units)
|
||||
* delta = size of atom displacements (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all numdiff 1 0.0001
|
||||
fix 1 all numdiff 10 1e-6
|
||||
fix 1 all numdiff 100 0.01
|
||||
fix 1 movegroup numdiff 100 0.01
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -67,16 +66,17 @@ by two times *delta*.
|
||||
|
||||
The cost of each energy evaluation is essentially the cost of an MD
|
||||
timestep. Thus invoking this fix once for a 3d system has a cost
|
||||
of 6N timesteps, where N is the total number of atoms in the system
|
||||
(assuming all atoms are included in the group). So this fix can be
|
||||
very expensive to use for large systems.
|
||||
of 6N timesteps, where N is the total number of atoms in the system.
|
||||
So this fix can be very expensive to use for large systems.
|
||||
One expedient alternative is to define the fix for a group containing
|
||||
only a few atoms.
|
||||
|
||||
----------
|
||||
|
||||
The *Nevery* argument specifies on what timesteps the force will
|
||||
be used calculated by finite difference.
|
||||
|
||||
The *delta* argument specifies the positional displacement each
|
||||
The *delta* argument specifies the size of the displacement each
|
||||
atom will undergo.
|
||||
|
||||
----------
|
||||
@ -93,7 +93,12 @@ This fix produces a per-atom array which can be accessed by various
|
||||
the force on each atom as calculated by finite difference. The
|
||||
per-atom values can only be accessed on timesteps that are multiples
|
||||
of *Nevery* since that is when the finite difference forces are
|
||||
calculated.
|
||||
calculated. See the examples in *examples/numdiff* directory
|
||||
to see how this fix can be used to directly compare with
|
||||
the analytic forces computed by LAMMPS.
|
||||
|
||||
The array values calculated by this compute
|
||||
will be in force :doc:`units <units>`.
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is invoked during :doc:`energy
|
||||
@ -108,7 +113,7 @@ was built with that package. See the :doc:`Build package <Build_package>` page
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`dynamical_matrix <dynamical_matrix>`,
|
||||
:doc:`dynamical_matrix <dynamical_matrix>`, :doc:`fix numdiff/virial <fix_numdiff_virial>`,
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
115
doc/src/fix_numdiff_virial.rst
Normal file
115
doc/src/fix_numdiff_virial.rst
Normal file
@ -0,0 +1,115 @@
|
||||
.. index:: fix numdiff/virial
|
||||
|
||||
fix numdiff/virial command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID numdiff/virial Nevery delta
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* numdiff/virial = style name of this fix command
|
||||
* Nevery = calculate virial by finite difference every this many timesteps
|
||||
* delta = magnitude of strain fields (dimensionless)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all numdiff/stress 10 1e-6
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Calculate the virial stress tensor through a finite difference calculation of
|
||||
energy versus strain. These values can be compared to the analytic virial
|
||||
tensor computed by pair styles, bond styles, etc. This can be useful for
|
||||
debugging or other purposes. The specified group must be "all".
|
||||
|
||||
This fix applies linear strain fields of magnitude *delta* to all the
|
||||
atoms relative to a point at the center of the box. The
|
||||
strain fields are in six different directions, corresponding to the
|
||||
six Cartesian components of the stress tensor defined by LAMMPS.
|
||||
For each direction it applies the strain field in both the positive
|
||||
and negative senses, and the new energy of the entire system
|
||||
is calculated after each. The difference in these two energies
|
||||
divided by two times *delta*, approximates the corresponding
|
||||
component of the virial stress tensor, after applying
|
||||
a suitable unit conversion.
|
||||
|
||||
.. note::
|
||||
|
||||
It is important to choose a suitable value for delta, the magnitude of
|
||||
strains that are used to generate finite difference
|
||||
approximations to the exact virial stress. For typical systems, a value in
|
||||
the range of 1 part in 1e5 to 1e6 will be sufficient.
|
||||
However, the best value will depend on a multitude of factors
|
||||
including the stiffness of the interatomic potential, the thermodynamic
|
||||
state of the material being probed, and so on. The only way to be sure
|
||||
that you have made a good choice is to do a sensitivity study on a
|
||||
representative atomic configuration, sweeping over a wide range of
|
||||
values of delta. If delta is too small, the output values will vary
|
||||
erratically due to truncation effects. If delta is increased beyond a
|
||||
certain point, the output values will start to vary smoothly with
|
||||
delta, due to growing contributions from higher order derivatives. In
|
||||
between these two limits, the numerical virial values should be largely
|
||||
independent of delta.
|
||||
|
||||
----------
|
||||
|
||||
The *Nevery* argument specifies on what timesteps the force will
|
||||
be used calculated by finite difference.
|
||||
|
||||
The *delta* argument specifies the size of the displacement each
|
||||
atom will undergo.
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files
|
||||
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
|
||||
relevant to this fix.
|
||||
|
||||
This fix produces a global vector which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`, which stores the components of
|
||||
the virial stress tensor as calculated by finite difference. The
|
||||
global vector can only be accessed on timesteps that are multiples
|
||||
of *Nevery* since that is when the finite difference virial is
|
||||
calculated. See the examples in *examples/numdiff* directory
|
||||
to see how this fix can be used to directly compare with
|
||||
the analytic virial stress tensor computed by LAMMPS.
|
||||
|
||||
The order of the virial stress tensor components is *xx*, *yy*, *zz*,
|
||||
*yz*, *xz*, and *xy*, consistent with Voigt notation. Note that
|
||||
the vector produced by :doc:`compute pressure <compute_pressure>`
|
||||
uses a different ordering, with *yz* and *xy* swapped.
|
||||
|
||||
The vector values calculated by this compute are
|
||||
"intensive". The vector values will be in pressure
|
||||
:doc:`units <units>`.
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is invoked during :doc:`energy
|
||||
minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the EXTRA-FIX package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix numdiff <fix_numdiff>`, :doc:`compute pressure <compute_pressure>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -66,7 +66,10 @@ equivalent to Newton's equations of motion for shear flow by
|
||||
:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
|
||||
the desired velocity gradient and the correct production of work by
|
||||
stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
|
||||
<Daivis>`. As implemented in LAMMPS, they are coupled to a
|
||||
<Daivis>`.
|
||||
The LAMMPS implementation corresponds to the p-SLLOD variant
|
||||
of SLLOD. :ref:`(Edwards) <Edwards>`.
|
||||
The equations of motion are coupled to a
|
||||
Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
|
||||
following the implementation used for the :doc:`fix nvt <fix_nh>`
|
||||
command.
|
||||
@ -180,6 +183,10 @@ Same as :doc:`fix nvt <fix_nh>`, except tchain = 1.
|
||||
|
||||
**(Daivis and Todd)** Daivis and Todd, J Chem Phys, 124, 194103 (2006).
|
||||
|
||||
.. _Edwards:
|
||||
|
||||
**(Edwards)** Edwards, Baig, and Keffer, J Chem Phys 124, 194104 (2006).
|
||||
|
||||
.. _Daivis-sllod:
|
||||
|
||||
**(Daivis and Todd)** Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
|
||||
|
||||
@ -108,10 +108,11 @@ fluid, in appropriate units. See the :ref:`Muller-Plathe paper <Muller-Plathe2>
|
||||
|
||||
An alternative method for calculating a viscosity is to run a NEMD
|
||||
simulation, as described on the :doc:`Howto nemd <Howto_nemd>` doc page.
|
||||
NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command. Thus they cannot be run on a charged
|
||||
system using a :doc:`PPPM solver <kspace_style>` since PPPM does not
|
||||
currently support non-orthogonal boxes. Using fix viscosity keeps the
|
||||
box orthogonal; thus it does not suffer from this limitation.
|
||||
NEMD simulations deform the simulation box via the :doc:`fix deform <fix_deform>` command.
|
||||
|
||||
Some features or combination of settings in LAMMPS do not support
|
||||
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
|
||||
thus it does not suffer from these limitations.
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
@ -460,7 +460,7 @@ using *neigh/thread* *on*, a full neighbor list must also be used. Using
|
||||
is turned on by default only when there are 16K atoms or less owned by
|
||||
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
|
||||
potentials support this keyword yet, and only thread over atoms. Many
|
||||
simple pair-wise potentials such as Lennard-Jones do support threading
|
||||
simple pairwise potentials such as Lennard-Jones do support threading
|
||||
over both atoms and neighbors.
|
||||
|
||||
The *newton* keyword sets the Newton flags for pairwise and bonded
|
||||
|
||||
@ -119,7 +119,7 @@ name are the older, original LAMMPS implementations. They compute the
|
||||
LJ and Coulombic interactions with an energy switching function (esw,
|
||||
shown in the formula below as S(r)), which ramps the energy smoothly
|
||||
to zero between the inner and outer cutoff. This can cause
|
||||
irregularities in pair-wise forces (due to the discontinuous second
|
||||
irregularities in pairwise forces (due to the discontinuous second
|
||||
derivative of energy at the boundaries of the switching region), which
|
||||
in some cases can result in detectable artifacts in an MD simulation.
|
||||
|
||||
|
||||
@ -50,7 +50,7 @@ Style *dpd* computes a force field for dissipative particle dynamics
|
||||
|
||||
Style *dpd/tstat* invokes a DPD thermostat on pairwise interactions,
|
||||
which is equivalent to the non-conservative portion of the DPD force
|
||||
field. This pair-wise thermostat can be used in conjunction with any
|
||||
field. This pairwise thermostat can be used in conjunction with any
|
||||
:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
|
||||
like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
|
||||
Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use
|
||||
|
||||
@ -164,7 +164,7 @@ Following the *LJCutMelt* example, here are the two functions:
|
||||
.. note::
|
||||
|
||||
The evaluation of scripted python code will slow down the
|
||||
computation pair-wise interactions quite significantly. However, this
|
||||
computation pairwise interactions quite significantly. However, this
|
||||
can be largely worked around through using the python pair style not
|
||||
for the actual simulation, but to generate tabulated potentials on the
|
||||
fly using the :doc:`pair_write <pair_write>` command. Please see below
|
||||
|
||||
@ -154,10 +154,10 @@ accelerated styles exist.
|
||||
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
|
||||
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
|
||||
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
|
||||
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting with generalized force field
|
||||
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field
|
||||
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
|
||||
* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
|
||||
* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting
|
||||
* :doc:`dpd/tstat <pair_dpd>` - pairwise DPD thermostatting
|
||||
* :doc:`dsmc <pair_dsmc>` - Direct Simulation Monte Carlo (DSMC)
|
||||
* :doc:`e3b <pair_e3b>` - Explicit-three body (E3B) water model
|
||||
* :doc:`drip <pair_drip>` - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
|
||||
|
||||
@ -202,7 +202,7 @@ elements are the same. Thus the two-body parameters for Si
|
||||
interacting with C, comes from the SiCC entry. The three-body
|
||||
parameters can in principle be specific to the three elements of the
|
||||
configuration. In the literature, however, the three-body parameters
|
||||
are usually defined by simple formulas involving two sets of pair-wise
|
||||
are usually defined by simple formulas involving two sets of pairwise
|
||||
parameters, corresponding to the ij and ik pairs, where i is the
|
||||
center atom. The user must ensure that the correct combining rule is
|
||||
used to calculate the values of the three-body parameters for
|
||||
|
||||
@ -76,8 +76,10 @@ must be set before this command can be invoked.
|
||||
Due to how the pairwise force is computed, an inner value > 0.0 must
|
||||
be specified even if the potential has a finite value at r = 0.0.
|
||||
|
||||
For EAM potentials, the pair_write command only tabulates the
|
||||
pairwise portion of the potential, not the embedding portion.
|
||||
The *pair_write* command can only be used for pairwise additive
|
||||
interactions for which a `Pair::single()` function can be and has
|
||||
been implemented. This excludes for example manybody potentials
|
||||
or TIP4P coulomb styles.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -89,7 +89,7 @@ in its 3d FFTs. In this scenario, splitting your P total processors
|
||||
into 2 subsets of processors, P1 in the first partition and P2 in the
|
||||
second partition, can enable your simulation to run faster. This is
|
||||
because the long-range forces in PPPM can be calculated at the same
|
||||
time as pair-wise and bonded forces are being calculated, and the FFTs
|
||||
time as pairwise and bonded forces are being calculated, and the FFTs
|
||||
can actually speed up when running on fewer processors.
|
||||
|
||||
To use this style, you must define 2 partitions where P1 is a multiple
|
||||
|
||||
@ -194,6 +194,7 @@ Baczewski
|
||||
Bagchi
|
||||
Bagi
|
||||
Bagnold
|
||||
Baig
|
||||
Bajaj
|
||||
Bkappa
|
||||
Bal
|
||||
@ -668,6 +669,7 @@ Derlet
|
||||
Deserno
|
||||
Destree
|
||||
destructor
|
||||
destructors
|
||||
detils
|
||||
Devanathan
|
||||
devel
|
||||
@ -1569,6 +1571,7 @@ ke
|
||||
KE
|
||||
Keblinski
|
||||
Keefe
|
||||
Keffer
|
||||
keflag
|
||||
Keir
|
||||
Kelchner
|
||||
@ -2647,6 +2650,7 @@ pscreen
|
||||
pscrozi
|
||||
pseudodynamics
|
||||
pseudopotential
|
||||
pSp
|
||||
Pstart
|
||||
Pstop
|
||||
pstyle
|
||||
@ -2925,6 +2929,7 @@ Runge
|
||||
runtime
|
||||
Rutuparna
|
||||
rx
|
||||
rxd
|
||||
rxnave
|
||||
rxnsum
|
||||
ry
|
||||
|
||||
@ -94,7 +94,7 @@ msst: MSST shock dynamics
|
||||
nb3b: use of nonbonded 3-body harmonic pair style
|
||||
neb: nudged elastic band (NEB) calculation for barrier finding
|
||||
nemd: non-equilibrium MD of 2d sheared system
|
||||
numdiff: numerical difference computation of forces
|
||||
numdiff: numerical difference computation of forces and virial
|
||||
obstacle: flow around two voids in a 2d channel
|
||||
peptide: dynamics of a small solvated peptide chain (5-mer)
|
||||
peri: Peridynamic model of cylinder impacted by indenter
|
||||
|
||||
43
examples/cij_nvt/in.ljfcc
Normal file
43
examples/cij_nvt/in.ljfcc
Normal file
@ -0,0 +1,43 @@
|
||||
# Numerical difference calculation
|
||||
# of Born matrix
|
||||
|
||||
# Note that because of cubic symmetry and central forces, we have:
|
||||
# C11, pure axial == positive mean value: 1,2,3
|
||||
# C44==C23, pure shear == positive mean value, exactly match in pairs: (4,12),(5,8),(6,7)
|
||||
# C14==C56, shear/axial(normal) == zero mean, exactly match in pairs: (9,21),(14,20),(18,19)
|
||||
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 50 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable delta index 1.0e-6 # strain size
|
||||
variable temp index 0.3 # temperature
|
||||
variable rho index 0.8442 # reduced density
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create ${temp} 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute born all born/matrix
|
||||
thermo ${nthermo}
|
||||
thermo_style custom step temp pe press c_born[*]
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
51
examples/cij_nvt/in.ljfcc_both
Normal file
51
examples/cij_nvt/in.ljfcc_both
Normal file
@ -0,0 +1,51 @@
|
||||
# Numerical difference calculation
|
||||
# of Born matrix
|
||||
|
||||
# Note that because of cubic symmetry and central forces, we have:
|
||||
# C11, pure axial == positive mean value: 1,2,3
|
||||
# C44==C23, pure shear == positive mean value, (exactly) match in pairs: (4,12),(5,8),(6,7)
|
||||
# C14==C56, shear/axial(normal) == zero mean, (exactly) match in pairs: (9,21),(14,20),(18,19)
|
||||
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||
# the "(exactly)" above is because these symmetries seem to be sensitive to details
|
||||
# of how the finite shear deformations are applied
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 50 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable delta index 1.0e-8 # strain size
|
||||
variable temp index 0.3 # temperature
|
||||
variable rho index 0.8442 # reduced density
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create ${temp} 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute myvirial all pressure NULL virial
|
||||
compute bornnum all born/matrix numdiff ${delta} myvirial
|
||||
compute born all born/matrix
|
||||
variable bornrel vector 1.0-c_bornnum/c_born
|
||||
|
||||
thermo ${nthermo}
|
||||
thermo_style custom step temp pe press &
|
||||
v_bornrel[1] v_bornrel[2] v_bornrel[3] v_bornrel[4] v_bornrel[5] v_bornrel[6] v_bornrel[7] v_bornrel[8] v_bornrel[9] v_bornrel[10] v_bornrel[11] v_bornrel[12] v_bornrel[13] v_bornrel[14] v_bornrel[15] v_bornrel[16] v_bornrel[17] v_bornrel[18] v_bornrel[19] v_bornrel[20] v_bornrel[21]
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
47
examples/cij_nvt/in.ljfcc_num
Normal file
47
examples/cij_nvt/in.ljfcc_num
Normal file
@ -0,0 +1,47 @@
|
||||
# Numerical difference calculation
|
||||
# of Born matrix
|
||||
|
||||
# Note that because of cubic symmetry and central forces, we have:
|
||||
# C11, pure axial == positive mean value: 1,2,3
|
||||
# C44==C23, pure shear == positive mean value, (exactly) match in pairs: (4,12),(5,8),(6,7)
|
||||
# C14==C56, shear/axial(normal) == zero mean, (exactly) match in pairs: (9,21),(14,20),(18,19)
|
||||
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||
# the "(exactly)" above is because these symmetries seem to be sensitive to details
|
||||
# of how the finite shear deformations are applied
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 50 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable delta index 1.0e-6 # strain size
|
||||
variable temp index 0.3 # temperature
|
||||
variable rho index 0.8442 # reduced density
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create ${temp} 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute myvirial all pressure NULL virial
|
||||
compute born all born/matrix numdiff ${delta} myvirial
|
||||
thermo ${nthermo}
|
||||
thermo_style custom step temp pe press c_born[*]
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
102
examples/cij_nvt/log.29Jan2022.born.g++.1
Normal file
102
examples/cij_nvt/log.29Jan2022.born.g++.1
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (7 Jan 2022)
|
||||
# Numerical difference calculation
|
||||
# of Born matrix
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 50 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable delta index 1.0e-6 # strain size
|
||||
variable temp index 0.3 # temperature
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 3 0 ${nlat}
|
||||
region box block 0 3 0 3 0 3
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 108 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create ${temp} 87287 loop geom
|
||||
velocity all create 0.3 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute born all born/matrix
|
||||
thermo ${nthermo}
|
||||
thermo 10
|
||||
thermo_style custom step temp pe press c_born[*]
|
||||
|
||||
run ${nsteps}
|
||||
run 50
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.5
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 1.25, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) compute born/matrix, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.574 | 2.574 | 2.574 Mbytes
|
||||
Step Temp PotEng Press c_born[1] c_born[2] c_born[3] c_born[4] c_born[5] c_born[6] c_born[7] c_born[8] c_born[9] c_born[10] c_born[11] c_born[12] c_born[13] c_born[14] c_born[15] c_born[16] c_born[17] c_born[18] c_born[19] c_born[20] c_born[21]
|
||||
0 0.3 -6.7733681 -5.9844023 411.5161 411.5161 411.5161 595.57522 595.57522 595.57522 595.57522 595.57522 -2.7200464e-15 -6.1062266e-15 7.7715612e-16 595.57522 -1.1518564e-14 -3.3306691e-15 -5.3013149e-15 -1.0630385e-14 -6.800116e-15 -2.6367797e-15 -3.4139358e-15 -3.7747583e-15 -2.7200464e-15
|
||||
10 0.25283594 -6.703292 -5.5569889 891.93989 928.15437 944.55768 872.69866 852.24088 816.0675 816.0675 852.24088 10.111334 3.6921122 -6.3839362 872.69866 -4.6709643 4.4335317 -9.7018557 -4.5201548 3.7624526 11.200776 11.200776 4.4335317 10.111334
|
||||
20 0.13298345 -6.5218396 -4.5683635 1958.2215 2130.5784 2172.9636 1516.3032 1426.6019 1323.0834 1323.0834 1426.6019 39.867158 11.406477 -25.845853 1516.3032 3.3483658 27.179119 -36.809191 10.147948 7.0018777 41.995438 41.995438 27.179119 39.867158
|
||||
30 0.089302796 -6.4604227 -4.1807379 2401.2346 2625.1676 2638.9312 1724.973 1625.4639 1602.8817 1602.8817 1625.4639 55.594925 -101.03316 -41.689385 1724.973 35.280816 26.589804 -40.046683 63.973353 -78.086653 41.559746 41.559746 26.589804 55.594925
|
||||
40 0.12149354 -6.5076059 -4.4000835 2234.612 2345.8821 2337.9552 1513.845 1486.9674 1564.2263 1564.2263 1486.9674 56.775913 -199.0226 -45.302207 1513.845 27.333643 -9.5839331 -16.768077 120.5015 -141.06684 17.802047 17.802047 -9.5839331 56.775913
|
||||
50 0.13053032 -6.5204024 -4.5064456 2097.1985 2270.3252 2180.7348 1458.5923 1396.6336 1507.4402 1507.4402 1396.6336 37.603097 -213.85355 22.82129 1458.5923 47.47204 -20.546302 54.328025 195.36071 -169.33495 -24.624815 -24.624815 -20.546302 37.603097
|
||||
Loop time of 0.00790344 on 1 procs for 50 steps with 108 atoms
|
||||
|
||||
Performance: 2732988.192 tau/day, 6326.362 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0014593 | 0.0014593 | 0.0014593 | 0.0 | 18.46
|
||||
Neigh | 0.0047863 | 0.0047863 | 0.0047863 | 0.0 | 60.56
|
||||
Comm | 0.00057975 | 0.00057975 | 0.00057975 | 0.0 | 7.34
|
||||
Output | 0.00096954 | 0.00096954 | 0.00096954 | 0.0 | 12.27
|
||||
Modify | 5.3432e-05 | 5.3432e-05 | 5.3432e-05 | 0.0 | 0.68
|
||||
Other | | 5.508e-05 | | | 0.70
|
||||
|
||||
Nlocal: 108 ave 108 max 108 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 700 ave 700 max 700 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2909 ave 2909 max 2909 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2909
|
||||
Ave neighs/atom = 26.935185
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:00
|
||||
102
examples/cij_nvt/log.29Jan2022.born.g++.4
Normal file
102
examples/cij_nvt/log.29Jan2022.born.g++.4
Normal file
@ -0,0 +1,102 @@
|
||||
LAMMPS (7 Jan 2022)
|
||||
# Numerical difference calculation
|
||||
# of Born matrix
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 50 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable delta index 1.0e-6 # strain size
|
||||
variable temp index 0.3 # temperature
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 3 0 ${nlat}
|
||||
region box block 0 3 0 3 0 3
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 108 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create ${temp} 87287 loop geom
|
||||
velocity all create 0.3 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute born all born/matrix
|
||||
thermo ${nthermo}
|
||||
thermo 10
|
||||
thermo_style custom step temp pe press c_born[*]
|
||||
|
||||
run ${nsteps}
|
||||
run 50
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.5
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 1.25, bins = 5 5 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) compute born/matrix, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.561 | 2.561 | 2.561 Mbytes
|
||||
Step Temp PotEng Press c_born[1] c_born[2] c_born[3] c_born[4] c_born[5] c_born[6] c_born[7] c_born[8] c_born[9] c_born[10] c_born[11] c_born[12] c_born[13] c_born[14] c_born[15] c_born[16] c_born[17] c_born[18] c_born[19] c_born[20] c_born[21]
|
||||
0 0.3 -6.7733681 -5.9844023 411.5161 411.5161 411.5161 595.57522 595.57522 595.57522 595.57522 595.57522 -2.9143354e-15 -1.9984014e-15 1.8873791e-15 595.57522 -9.7560848e-15 -3.3029135e-15 -9.6311847e-15 -1.2281842e-14 -5.3568261e-15 -2.5257574e-15 -3.2196468e-15 -3.5804693e-15 -2.553513e-15
|
||||
10 0.25283594 -6.703292 -5.5569889 891.93989 928.15437 944.55768 872.69866 852.24088 816.0675 816.0675 852.24088 10.111334 3.6921122 -6.3839362 872.69866 -4.6709643 4.4335317 -9.7018557 -4.5201548 3.7624526 11.200776 11.200776 4.4335317 10.111334
|
||||
20 0.13298345 -6.5218396 -4.5683635 1958.2215 2130.5784 2172.9636 1516.3032 1426.6019 1323.0834 1323.0834 1426.6019 39.867158 11.406477 -25.845853 1516.3032 3.3483658 27.179119 -36.809191 10.147948 7.0018777 41.995438 41.995438 27.179119 39.867158
|
||||
30 0.089302796 -6.4604227 -4.1807379 2401.2346 2625.1676 2638.9312 1724.973 1625.4639 1602.8817 1602.8817 1625.4639 55.594925 -101.03316 -41.689385 1724.973 35.280816 26.589804 -40.046683 63.973353 -78.086653 41.559746 41.559746 26.589804 55.594925
|
||||
40 0.12149354 -6.5076059 -4.4000835 2234.612 2345.8821 2337.9552 1513.845 1486.9674 1564.2263 1564.2263 1486.9674 56.775913 -199.0226 -45.302207 1513.845 27.333643 -9.5839331 -16.768077 120.5015 -141.06684 17.802047 17.802047 -9.5839331 56.775913
|
||||
50 0.13053032 -6.5204024 -4.5064456 2097.1985 2270.3252 2180.7348 1458.5923 1396.6336 1507.4402 1507.4402 1396.6336 37.603097 -213.85355 22.82129 1458.5923 47.47204 -20.546302 54.328025 195.36071 -169.33495 -24.624815 -24.624815 -20.546302 37.603097
|
||||
Loop time of 0.00293746 on 4 procs for 50 steps with 108 atoms
|
||||
|
||||
Performance: 7353280.980 tau/day, 17021.484 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00037884 | 0.00040147 | 0.00041828 | 0.0 | 13.67
|
||||
Neigh | 0.0010222 | 0.0011142 | 0.0011623 | 0.2 | 37.93
|
||||
Comm | 0.00098867 | 0.0010309 | 0.0011341 | 0.2 | 35.09
|
||||
Output | 0.00030288 | 0.00031473 | 0.00034979 | 0.0 | 10.71
|
||||
Modify | 2.0147e-05 | 2.218e-05 | 2.3691e-05 | 0.0 | 0.76
|
||||
Other | | 5.406e-05 | | | 1.84
|
||||
|
||||
Nlocal: 27 ave 31 max 25 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 429.75 ave 450 max 409 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 727.25 ave 845 max 651 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2909
|
||||
Ave neighs/atom = 26.935185
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,33 +1,74 @@
|
||||
# Numerical difference calculation of error in forces
|
||||
# Numerical difference calculation
|
||||
# of error in forces and virial stress
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
# adjustable parameters
|
||||
|
||||
atom_modify map yes
|
||||
lattice fcc 5.358000
|
||||
region box block 0 6 0 6 0 6
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 39.903
|
||||
variable nsteps index 500 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable ndump index 500 # dump output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable fdelta index 1.0e-4 # displacement size
|
||||
variable vdelta index 1.0e-6 # strain size
|
||||
variable temp index 10.0 # temperature
|
||||
|
||||
velocity all create 10 2357 mom yes dist gaussian
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
atom_modify map yes
|
||||
lattice fcc 5.358000
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 39.903
|
||||
|
||||
neighbor 1 bin
|
||||
velocity all create ${temp} 2357 mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
|
||||
fix numdiff all numdiff 200 0.0001
|
||||
fix nve all nve
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
variable errx atom fx-f_numdiff[1]
|
||||
variable erry atom fy-f_numdiff[2]
|
||||
variable errz atom fz-f_numdiff[3]
|
||||
timestep 0.001
|
||||
fix nve all nve
|
||||
|
||||
write_dump all custom tmp.error f_numdiff[1] f_numdiff[2] f_numdiff[3]
|
||||
# define numerical force calculation
|
||||
|
||||
dump forces all custom 200 force_error.dump v_errx v_erry v_errz
|
||||
thermo 200
|
||||
run 2000
|
||||
fix numforce all numdiff ${nthermo} ${fdelta}
|
||||
variable ferrx atom f_numforce[1]-fx
|
||||
variable ferry atom f_numforce[2]-fy
|
||||
variable ferrz atom f_numforce[3]-fz
|
||||
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
||||
compute faverrsq all reduce ave v_ferrsq
|
||||
variable fsq atom fx^2+fy^2+fz^2
|
||||
compute favsq all reduce ave v_fsq
|
||||
variable frelerr equal sqrt(c_faverrsq/c_favsq)
|
||||
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
||||
|
||||
# define numerical virial stress tensor calculation
|
||||
|
||||
compute myvirial all pressure NULL virial
|
||||
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
||||
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
||||
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
||||
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
||||
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
||||
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
||||
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
||||
variable verrsq equal "v_errxx^2 + &
|
||||
v_erryy^2 + &
|
||||
v_errzz^2 + &
|
||||
v_erryz^2 + &
|
||||
v_errxz^2 + &
|
||||
v_errxy^2"
|
||||
variable vsq equal "c_myvirial[1]^2 + &
|
||||
c_myvirial[3]^2 + &
|
||||
c_myvirial[3]^2 + &
|
||||
c_myvirial[4]^2 + &
|
||||
c_myvirial[5]^2 + &
|
||||
c_myvirial[6]^2"
|
||||
variable vrelerr equal sqrt(v_verrsq/v_vsq)
|
||||
|
||||
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
|
||||
thermo ${nthermo}
|
||||
run ${nsteps}
|
||||
|
||||
175
examples/numdiff/log.28Jan2022.log.numdiff.g++.1
Normal file
175
examples/numdiff/log.28Jan2022.log.numdiff.g++.1
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (7 Jan 2022)
|
||||
# Numerical difference calculation
|
||||
# of error in forces and virial stress
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 500 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable ndump index 500 # dump output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable fdelta index 1.0e-4 # displacement size
|
||||
variable vdelta index 1.0e-6 # strain size
|
||||
variable temp index 10.0 # temperature
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map yes
|
||||
lattice fcc 5.358000
|
||||
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 3 0 ${nlat}
|
||||
region box block 0 3 0 3 0 3
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 108 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 39.903
|
||||
|
||||
velocity all create ${temp} 2357 mom yes dist gaussian
|
||||
velocity all create 10.0 2357 mom yes dist gaussian
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
timestep 0.001
|
||||
fix nve all nve
|
||||
|
||||
# define numerical force calculation
|
||||
|
||||
fix numforce all numdiff ${nthermo} ${fdelta}
|
||||
fix numforce all numdiff 10 ${fdelta}
|
||||
fix numforce all numdiff 10 1.0e-4
|
||||
variable ferrx atom f_numforce[1]-fx
|
||||
variable ferry atom f_numforce[2]-fy
|
||||
variable ferrz atom f_numforce[3]-fz
|
||||
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
||||
compute faverrsq all reduce ave v_ferrsq
|
||||
variable fsq atom fx^2+fy^2+fz^2
|
||||
compute favsq all reduce ave v_fsq
|
||||
variable frelerr equal sqrt(c_faverrsq/c_favsq)
|
||||
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
||||
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
||||
|
||||
# define numerical virial stress tensor calculation
|
||||
|
||||
compute myvirial all pressure NULL virial
|
||||
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
||||
fix numvirial all numdiff/virial 10 ${vdelta}
|
||||
fix numvirial all numdiff/virial 10 1.0e-6
|
||||
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
||||
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
||||
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
||||
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
||||
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
||||
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
||||
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
||||
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
||||
variable vrelerr equal sqrt(v_verrsq/v_vsq)
|
||||
|
||||
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
|
||||
thermo ${nthermo}
|
||||
thermo 10
|
||||
run ${nsteps}
|
||||
run 500
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.9407173
|
||||
ghost atom cutoff = 5.9407173
|
||||
binsize = 2.9703587, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes
|
||||
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
|
||||
0 10 -7.0259569 -6.8876486 28.564278 19203.344 1.5660292e-06
|
||||
10 9.9376583 -7.0250947 -6.8876486 30.254762 1.5040965e-08 2.1991382e-07
|
||||
20 9.7520139 -7.022527 -6.8876485 35.28505 1.4756358e-08 2.6265315e-06
|
||||
30 9.4477557 -7.0183188 -6.8876485 43.519863 1.4688198e-08 2.6356166e-07
|
||||
40 9.0330215 -7.0125826 -6.8876484 54.727797 1.4637921e-08 5.2292327e-08
|
||||
50 8.5192918 -7.0054772 -6.8876483 68.585553 1.4587854e-08 7.1324716e-08
|
||||
60 7.9212026 -6.997205 -6.8876481 84.684636 1.4525561e-08 3.1108149e-08
|
||||
70 7.2562592 -6.9880081 -6.8876479 102.54088 1.450885e-08 3.2311094e-08
|
||||
80 6.5444294 -6.9781627 -6.8876478 121.60715 1.4444738e-08 2.1776998e-08
|
||||
90 5.8075961 -6.9679715 -6.8876476 141.2895 1.4493562e-08 2.0400898e-08
|
||||
100 5.0688629 -6.957754 -6.8876474 160.9668 1.445455e-08 1.2636688e-08
|
||||
110 4.3517145 -6.947835 -6.8876472 180.0135 1.4460371e-08 1.2528038e-08
|
||||
120 3.6790589 -6.9385314 -6.887647 197.82486 1.4371757e-08 1.4489522e-08
|
||||
130 3.0721984 -6.9301379 -6.8876468 213.84331 1.4364708e-08 1.2461922e-08
|
||||
140 2.5497991 -6.9229125 -6.8876467 227.58429 1.4330926e-08 9.3913926e-09
|
||||
150 2.1269443 -6.917064 -6.8876466 238.6596 1.4287002e-08 4.1510266e-09
|
||||
160 1.8143642 -6.9127407 -6.8876465 246.79599 1.4282669e-08 7.7048281e-09
|
||||
170 1.6179191 -6.9100237 -6.8876465 251.84748 1.42726e-08 1.2719973e-08
|
||||
180 1.5383946 -6.9089239 -6.8876466 253.79991 1.4236534e-08 8.1200831e-09
|
||||
190 1.5716287 -6.9093836 -6.8876467 252.76745 1.41706e-08 6.5670612e-09
|
||||
200 1.7089493 -6.911283 -6.8876468 248.98142 1.4096463e-08 1.1685863e-08
|
||||
210 1.9378716 -6.9144493 -6.8876469 242.77289 1.4008978e-08 1.1226902e-08
|
||||
220 2.2429731 -6.9186692 -6.887647 234.55055 1.3886901e-08 9.9914102e-09
|
||||
230 2.606862 -6.9237023 -6.8876472 224.77626 1.3864576e-08 1.1540228e-08
|
||||
240 3.0111524 -6.9292941 -6.8876474 213.93996 1.3696314e-08 1.1697747e-08
|
||||
250 3.4373794 -6.9351893 -6.8876475 202.53583 1.3626701e-08 1.0398197e-08
|
||||
260 3.8678047 -6.9411426 -6.8876476 191.04084 1.3489489e-08 6.6603364e-09
|
||||
270 4.2860853 -6.9469279 -6.8876478 179.89646 1.3312014e-08 1.1687917e-08
|
||||
280 4.6777954 -6.9523457 -6.8876479 169.49404 1.3081144e-08 1.1336675e-08
|
||||
290 5.030805 -6.9572282 -6.887648 160.16371 1.2947385e-08 1.7342825e-08
|
||||
300 5.3355278 -6.9614428 -6.887648 152.16682 1.2893673e-08 1.7510534e-08
|
||||
310 5.5850532 -6.964894 -6.887648 145.69148 1.2842022e-08 1.2782546e-08
|
||||
320 5.7751794 -6.9675236 -6.8876481 140.85102 1.2903488e-08 1.5319437e-08
|
||||
330 5.9043601 -6.9693103 -6.887648 137.68497 1.3076809e-08 1.1208999e-08
|
||||
340 5.9735784 -6.9702676 -6.887648 136.16232 1.3296904e-08 1.891087e-08
|
||||
350 5.9861549 -6.9704415 -6.887648 136.18679 1.3504051e-08 2.5783601e-08
|
||||
360 5.947496 -6.9699067 -6.8876479 137.60397 1.3731112e-08 2.0556839e-08
|
||||
370 5.8647874 -6.9687627 -6.8876478 140.2101 1.4009878e-08 2.1771736e-08
|
||||
380 5.7466376 -6.9671285 -6.8876477 143.76234 1.4092054e-08 1.1085162e-08
|
||||
390 5.6026773 -6.9651374 -6.8876477 147.99019 1.4282872e-08 2.0221602e-08
|
||||
400 5.4431231 -6.9629305 -6.8876476 152.60787 1.4317739e-08 1.7076065e-08
|
||||
410 5.2783192 -6.960651 -6.8876475 157.32722 1.4415075e-08 2.5031776e-08
|
||||
420 5.1182723 -6.9584374 -6.8876474 161.87063 1.4441435e-08 2.2519289e-08
|
||||
430 4.9722 -6.956417 -6.8876473 165.98344 1.4550624e-08 2.4512613e-08
|
||||
440 4.8481153 -6.9547008 -6.8876473 169.44527 1.4544672e-08 1.4758301e-08
|
||||
450 4.7524707 -6.9533779 -6.8876472 172.07964 1.4546492e-08 1.324687e-08
|
||||
460 4.6898817 -6.9525122 -6.8876472 173.76132 1.4537475e-08 1.351367e-08
|
||||
470 4.6629495 -6.9521397 -6.8876472 174.42109 1.4530458e-08 1.521106e-08
|
||||
480 4.6721922 -6.9522675 -6.8876472 174.04742 1.4543785e-08 1.0905422e-08
|
||||
490 4.7160887 -6.9528747 -6.8876473 172.68525 1.4545591e-08 2.0128525e-08
|
||||
500 4.7912313 -6.953914 -6.8876473 170.43183 1.4438981e-08 1.6062775e-08
|
||||
Loop time of 0.837333 on 1 procs for 500 steps with 108 atoms
|
||||
|
||||
Performance: 51.592 ns/day, 0.465 hours/ns, 597.134 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0097726 | 0.0097726 | 0.0097726 | 0.0 | 1.17
|
||||
Neigh | 0.03095 | 0.03095 | 0.03095 | 0.0 | 3.70
|
||||
Comm | 0.005564 | 0.005564 | 0.005564 | 0.0 | 0.66
|
||||
Output | 0.0042451 | 0.0042451 | 0.0042451 | 0.0 | 0.51
|
||||
Modify | 0.78618 | 0.78618 | 0.78618 | 0.0 | 93.89
|
||||
Other | | 0.0006258 | | | 0.07
|
||||
|
||||
Nlocal: 108 ave 108 max 108 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 558 ave 558 max 558 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 972 ave 972 max 972 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 972
|
||||
Ave neighs/atom = 9
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
175
examples/numdiff/log.28Jan2022.log.numdiff.g++.4
Normal file
175
examples/numdiff/log.28Jan2022.log.numdiff.g++.4
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (7 Jan 2022)
|
||||
# Numerical difference calculation
|
||||
# of error in forces and virial stress
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
variable nsteps index 500 # length of run
|
||||
variable nthermo index 10 # thermo output interval
|
||||
variable ndump index 500 # dump output interval
|
||||
variable nlat index 3 # size of box
|
||||
variable fdelta index 1.0e-4 # displacement size
|
||||
variable vdelta index 1.0e-6 # strain size
|
||||
variable temp index 10.0 # temperature
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
atom_modify map yes
|
||||
lattice fcc 5.358000
|
||||
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 ${nlat} 0 ${nlat}
|
||||
region box block 0 3 0 3 0 ${nlat}
|
||||
region box block 0 3 0 3 0 3
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 108 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 39.903
|
||||
|
||||
velocity all create ${temp} 2357 mom yes dist gaussian
|
||||
velocity all create 10.0 2357 mom yes dist gaussian
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 0.0102701 3.42
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
timestep 0.001
|
||||
fix nve all nve
|
||||
|
||||
# define numerical force calculation
|
||||
|
||||
fix numforce all numdiff ${nthermo} ${fdelta}
|
||||
fix numforce all numdiff 10 ${fdelta}
|
||||
fix numforce all numdiff 10 1.0e-4
|
||||
variable ferrx atom f_numforce[1]-fx
|
||||
variable ferry atom f_numforce[2]-fy
|
||||
variable ferrz atom f_numforce[3]-fz
|
||||
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
||||
compute faverrsq all reduce ave v_ferrsq
|
||||
variable fsq atom fx^2+fy^2+fz^2
|
||||
compute favsq all reduce ave v_fsq
|
||||
variable frelerr equal sqrt(c_faverrsq/c_favsq)
|
||||
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
||||
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
||||
|
||||
# define numerical virial stress tensor calculation
|
||||
|
||||
compute myvirial all pressure NULL virial
|
||||
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
||||
fix numvirial all numdiff/virial 10 ${vdelta}
|
||||
fix numvirial all numdiff/virial 10 1.0e-6
|
||||
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
||||
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
||||
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
||||
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
||||
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
||||
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
||||
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
||||
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
||||
variable vrelerr equal sqrt(v_verrsq/v_vsq)
|
||||
|
||||
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
|
||||
thermo ${nthermo}
|
||||
thermo 10
|
||||
run ${nsteps}
|
||||
run 500
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.9407173
|
||||
ghost atom cutoff = 5.9407173
|
||||
binsize = 2.9703587, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cubic, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes
|
||||
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
|
||||
0 10 -7.0259569 -6.8876486 28.564278 10664.391 9.1481187e-08
|
||||
10 9.9388179 -7.0251107 -6.8876486 30.21736 1.4771865e-08 1.3452512e-07
|
||||
20 9.7572185 -7.022599 -6.8876485 35.123527 1.437525e-08 8.0966999e-07
|
||||
30 9.4606673 -7.0184974 -6.8876484 43.132052 1.4375468e-08 1.990012e-08
|
||||
40 9.0579092 -7.0129268 -6.8876483 54.000927 1.4350331e-08 1.7239028e-08
|
||||
50 8.5607685 -7.0060508 -6.8876482 67.403151 1.4353284e-08 7.813181e-09
|
||||
60 7.9838726 -6.9980717 -6.8876481 82.935358 1.4398078e-08 2.022316e-08
|
||||
70 7.3442875 -6.9892255 -6.8876479 100.12892 1.434409e-08 7.5938179e-09
|
||||
80 6.6610579 -6.9797757 -6.8876477 118.46358 1.4324787e-08 7.1972571e-09
|
||||
90 5.9546462 -6.9700053 -6.8876476 137.38365 1.4322718e-08 4.3978378e-09
|
||||
100 5.2462727 -6.9602077 -6.8876474 156.31651 1.4273172e-08 4.6728038e-09
|
||||
110 4.5571706 -6.9506767 -6.8876472 174.69294 1.4266163e-08 3.522225e-09
|
||||
120 3.9077807 -6.9416949 -6.887647 191.96859 1.42241e-08 3.5357511e-09
|
||||
130 3.3169241 -6.9335227 -6.8876469 207.64566 1.4203813e-08 2.5182488e-09
|
||||
140 2.8010028 -6.926387 -6.8876468 221.29333 1.4164215e-08 2.3112509e-09
|
||||
150 2.3732854 -6.9204712 -6.8876467 232.5658 1.4134122e-08 1.9368963e-09
|
||||
160 2.0433329 -6.9159076 -6.8876466 241.21647 1.4095473e-08 3.6806452e-09
|
||||
170 1.8166184 -6.912772 -6.8876466 247.10715 1.4049531e-08 2.5319322e-09
|
||||
180 1.6943727 -6.9110813 -6.8876467 250.21143 1.3997912e-08 1.952404e-09
|
||||
190 1.6736731 -6.910795 -6.8876467 250.61203 1.3915487e-08 1.4271767e-09
|
||||
200 1.7477659 -6.9118199 -6.8876468 248.49223 1.3850618e-08 2.4515718e-09
|
||||
210 1.9065921 -6.9140167 -6.8876469 244.12226 1.3747916e-08 1.7957531e-09
|
||||
220 2.1374676 -6.91721 -6.887647 237.84173 1.3674779e-08 2.6613511e-09
|
||||
230 2.4258607 -6.9211989 -6.8876472 230.0395 1.3565712e-08 3.0777067e-09
|
||||
240 2.7562034 -6.9257679 -6.8876473 221.13265 1.3440442e-08 1.7111501e-09
|
||||
250 3.1126827 -6.9306984 -6.8876474 211.54566 1.3270914e-08 1.6690112e-09
|
||||
260 3.4799641 -6.9357784 -6.8876476 201.69126 1.3105092e-08 2.1637558e-09
|
||||
270 3.8438148 -6.9408108 -6.8876477 191.95361 1.2962846e-08 4.4613506e-09
|
||||
280 4.191607 -6.9456212 -6.8876478 182.6745 1.2846383e-08 3.3730203e-09
|
||||
290 4.5126922 -6.9500621 -6.8876478 174.14285 1.2710692e-08 2.2809889e-09
|
||||
300 4.7986487 -6.9540172 -6.8876479 166.58747 1.2657778e-08 6.9880891e-09
|
||||
310 5.0434083 -6.9574025 -6.8876479 160.17316 1.266381e-08 4.2486217e-09
|
||||
320 5.243275 -6.9601668 -6.8876479 154.99974 1.279856e-08 5.1505673e-09
|
||||
330 5.3968455 -6.9622908 -6.8876479 151.1038 1.2981831e-08 3.3339333e-09
|
||||
340 5.5048468 -6.9637845 -6.8876479 148.46296 1.3159021e-08 1.7881393e-09
|
||||
350 5.569902 -6.9646843 -6.8876479 147.00205 1.3439465e-08 5.6876219e-09
|
||||
360 5.5962378 -6.9650485 -6.8876478 146.60113 1.3645943e-08 7.233847e-09
|
||||
370 5.5893468 -6.9649531 -6.8876478 147.10471 1.3829581e-08 4.5514318e-09
|
||||
380 5.5556199 -6.9644866 -6.8876477 148.33195 1.4005893e-08 4.2971846e-09
|
||||
390 5.5019639 -6.9637444 -6.8876476 150.08725 1.4157454e-08 3.3564262e-09
|
||||
400 5.4354239 -6.962824 -6.8876476 152.17073 1.4226422e-08 4.2393923e-09
|
||||
410 5.3628267 -6.9618199 -6.8876475 154.38825 1.4302679e-08 3.8937698e-09
|
||||
420 5.2904639 -6.960819 -6.8876475 156.56034 1.4381099e-08 4.315875e-09
|
||||
430 5.2238282 -6.9598973 -6.8876474 158.52969 1.4426567e-08 4.2658185e-09
|
||||
440 5.1674149 -6.9591171 -6.8876474 160.16704 1.4453381e-08 5.7055268e-09
|
||||
450 5.1245913 -6.9585248 -6.8876474 161.37513 1.4449488e-08 4.4308801e-09
|
||||
460 5.0975361 -6.9581506 -6.8876474 162.09077 1.4445596e-08 5.8269923e-09
|
||||
470 5.0872416 -6.9580082 -6.8876474 162.28517 1.4444348e-08 4.8263194e-09
|
||||
480 5.0935712 -6.9580957 -6.8876474 161.96268 1.4411666e-08 6.222228e-09
|
||||
490 5.115362 -6.9583971 -6.8876474 161.15816 1.4369716e-08 3.3926077e-09
|
||||
500 5.1505605 -6.958884 -6.8876474 159.9333 1.4288515e-08 3.8845251e-09
|
||||
Loop time of 0.252598 on 4 procs for 500 steps with 108 atoms
|
||||
|
||||
Performance: 171.023 ns/day, 0.140 hours/ns, 1979.430 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0021545 | 0.0022845 | 0.0023794 | 0.2 | 0.90
|
||||
Neigh | 0.0063887 | 0.0067604 | 0.0069752 | 0.3 | 2.68
|
||||
Comm | 0.01048 | 0.010916 | 0.011408 | 0.3 | 4.32
|
||||
Output | 0.0026603 | 0.0027399 | 0.0029738 | 0.3 | 1.08
|
||||
Modify | 0.2295 | 0.22952 | 0.22954 | 0.0 | 90.86
|
||||
Other | | 0.0003814 | | | 0.15
|
||||
|
||||
Nlocal: 27 ave 29 max 25 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 325 ave 327 max 323 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 243 ave 273 max 228 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 972
|
||||
Ave neighs/atom = 9
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
@ -21,17 +21,17 @@ namespace LAMMPS_NS {
|
||||
class AngleZero2 : public Angle {
|
||||
public:
|
||||
AngleZero2(class LAMMPS *);
|
||||
virtual ~AngleZero2();
|
||||
virtual void compute(int, int);
|
||||
virtual void coeff(int, char **);
|
||||
virtual void settings(int, char **);
|
||||
~AngleZero2() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void settings(int, char **) override;
|
||||
|
||||
double equilibrium_angle(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_data(FILE *);
|
||||
double equilibrium_angle(int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
|
||||
double single(int, int, int, int);
|
||||
double single(int, int, int, int) override;
|
||||
|
||||
protected:
|
||||
double *theta0;
|
||||
|
||||
@ -21,18 +21,18 @@ namespace LAMMPS_NS {
|
||||
class BondZero2 : public Bond {
|
||||
public:
|
||||
BondZero2(class LAMMPS *);
|
||||
virtual ~BondZero2();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
~BondZero2() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
|
||||
void coeff(int, char **);
|
||||
double equilibrium_distance(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_data(FILE *);
|
||||
void coeff(int, char **) override;
|
||||
double equilibrium_distance(int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
|
||||
double single(int, double, int, int, double &);
|
||||
virtual void *extract(const char *, int &);
|
||||
double single(int, double, int, int, double &) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
double *r0;
|
||||
|
||||
@ -25,14 +25,14 @@ namespace LAMMPS_NS {
|
||||
class DihedralZero2 : public Dihedral {
|
||||
public:
|
||||
DihedralZero2(class LAMMPS *);
|
||||
virtual ~DihedralZero2();
|
||||
virtual void compute(int, int);
|
||||
virtual void coeff(int, char **);
|
||||
virtual void settings(int, char **);
|
||||
~DihedralZero2() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void settings(int, char **) override;
|
||||
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
|
||||
protected:
|
||||
int coeffflag;
|
||||
|
||||
@ -11,12 +11,6 @@
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve2, FixNVE2)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE2_H
|
||||
#define LMP_FIX_NVE2_H
|
||||
|
||||
@ -27,14 +21,14 @@ namespace LAMMPS_NS {
|
||||
class FixNVE2 : public Fix {
|
||||
public:
|
||||
FixNVE2(class LAMMPS *, int, char **);
|
||||
virtual ~FixNVE2() {}
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
virtual void initial_integrate_respa(int, int, int);
|
||||
virtual void final_integrate_respa(int, int);
|
||||
virtual void reset_dt();
|
||||
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
void initial_integrate_respa(int, int, int) override;
|
||||
void final_integrate_respa(int, int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
protected:
|
||||
double dtv, dtf;
|
||||
@ -44,7 +38,6 @@ class FixNVE2 : public Fix {
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
@ -21,14 +21,14 @@ namespace LAMMPS_NS {
|
||||
class ImproperZero2 : public Improper {
|
||||
public:
|
||||
ImproperZero2(class LAMMPS *);
|
||||
virtual ~ImproperZero2();
|
||||
virtual void compute(int, int);
|
||||
virtual void coeff(int, char **);
|
||||
virtual void settings(int, char **);
|
||||
~ImproperZero2() override;
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void settings(int, char **) override;
|
||||
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
|
||||
protected:
|
||||
int coeffflag;
|
||||
|
||||
@ -21,20 +21,20 @@ namespace LAMMPS_NS {
|
||||
class PairMorse2 : public Pair {
|
||||
public:
|
||||
PairMorse2(class LAMMPS *);
|
||||
virtual ~PairMorse2();
|
||||
virtual void compute(int, int);
|
||||
~PairMorse2() override;
|
||||
void compute(int, int) override;
|
||||
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
double single(int, int, int, int, double, double, double, double &) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
||||
@ -28,8 +28,8 @@ class PairMorse2OMP : public PairMorse2, public ThrOMP {
|
||||
public:
|
||||
PairMorse2OMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
void compute(int, int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
|
||||
@ -31,19 +31,19 @@ namespace LAMMPS_NS {
|
||||
class PairZero2 : public Pair {
|
||||
public:
|
||||
PairZero2(class LAMMPS *);
|
||||
virtual ~PairZero2();
|
||||
virtual void compute(int, int);
|
||||
virtual void compute_outer(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
~PairZero2() override;
|
||||
void compute(int, int) override;
|
||||
void compute_outer(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
double single(int, int, int, int, double, double, double, double &) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
||||
@ -30,12 +30,12 @@ class DumpAtomADIOS : public DumpAtom {
|
||||
|
||||
public:
|
||||
DumpAtomADIOS(class LAMMPS *, int, char **);
|
||||
virtual ~DumpAtomADIOS();
|
||||
~DumpAtomADIOS() override;
|
||||
|
||||
protected:
|
||||
virtual void openfile();
|
||||
virtual void write();
|
||||
virtual void init_style();
|
||||
void openfile() override;
|
||||
void write() override;
|
||||
void init_style() override;
|
||||
|
||||
private:
|
||||
DumpAtomADIOSInternal *internal;
|
||||
|
||||
@ -29,12 +29,12 @@ class DumpCustomADIOSInternal;
|
||||
class DumpCustomADIOS : public DumpCustom {
|
||||
public:
|
||||
DumpCustomADIOS(class LAMMPS *, int, char **);
|
||||
virtual ~DumpCustomADIOS();
|
||||
~DumpCustomADIOS() override;
|
||||
|
||||
protected:
|
||||
virtual void openfile();
|
||||
virtual void write();
|
||||
virtual void init_style();
|
||||
void openfile() override;
|
||||
void write() override;
|
||||
void init_style() override;
|
||||
|
||||
private:
|
||||
DumpCustomADIOSInternal *internal;
|
||||
|
||||
@ -34,18 +34,18 @@ class ReadADIOSInternal;
|
||||
class ReaderADIOS : public Reader {
|
||||
public:
|
||||
ReaderADIOS(class LAMMPS *);
|
||||
virtual ~ReaderADIOS();
|
||||
~ReaderADIOS() override;
|
||||
|
||||
virtual void settings(int, char **);
|
||||
void settings(int, char **) override;
|
||||
|
||||
virtual int read_time(bigint &);
|
||||
virtual void skip();
|
||||
virtual bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
|
||||
int &, int &, int &);
|
||||
virtual void read_atoms(int, int, double **);
|
||||
int read_time(bigint &) override;
|
||||
void skip() override;
|
||||
bigint read_header(double[3][3], int &, int &, int, int, int *, char **, int, int, int &,
|
||||
int &, int &, int &) override;
|
||||
void read_atoms(int, int, double **) override;
|
||||
|
||||
virtual void open_file(const char *);
|
||||
virtual void close_file();
|
||||
void open_file(const char *) override;
|
||||
void close_file() override;
|
||||
|
||||
private:
|
||||
int *fieldindex; // mapping of input fields to dump
|
||||
|
||||
@ -27,8 +27,8 @@ namespace LAMMPS_NS {
|
||||
class ComputeERotateAsphere : public Compute {
|
||||
public:
|
||||
ComputeERotateAsphere(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
double compute_scalar();
|
||||
void init() override;
|
||||
double compute_scalar() override;
|
||||
|
||||
private:
|
||||
double pfactor;
|
||||
|
||||
@ -27,16 +27,16 @@ namespace LAMMPS_NS {
|
||||
class ComputeTempAsphere : public Compute {
|
||||
public:
|
||||
ComputeTempAsphere(class LAMMPS *, int, char **);
|
||||
~ComputeTempAsphere();
|
||||
void init();
|
||||
void setup();
|
||||
double compute_scalar();
|
||||
void compute_vector();
|
||||
~ComputeTempAsphere() override;
|
||||
void init() override;
|
||||
void setup() override;
|
||||
double compute_scalar() override;
|
||||
void compute_vector() override;
|
||||
|
||||
void remove_bias(int, double *);
|
||||
void restore_bias(int, double *);
|
||||
void remove_bias_thr(int, double *, double *);
|
||||
void restore_bias_thr(int, double *, double *);
|
||||
void remove_bias(int, double *) override;
|
||||
void restore_bias(int, double *) override;
|
||||
void remove_bias_thr(int, double *, double *) override;
|
||||
void restore_bias_thr(int, double *, double *) override;
|
||||
|
||||
private:
|
||||
int mode;
|
||||
|
||||
@ -21,16 +21,15 @@ namespace LAMMPS_NS {
|
||||
class FixNHAsphere : public FixNH {
|
||||
public:
|
||||
FixNHAsphere(class LAMMPS *, int, char **);
|
||||
virtual ~FixNHAsphere() {}
|
||||
void init();
|
||||
void init() override;
|
||||
|
||||
protected:
|
||||
double dtq;
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
void nve_v();
|
||||
void nve_x();
|
||||
void nh_v_temp();
|
||||
void nve_v() override;
|
||||
void nve_x() override;
|
||||
void nh_v_temp() override;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,7 +27,6 @@ namespace LAMMPS_NS {
|
||||
class FixNPHAsphere : public FixNHAsphere {
|
||||
public:
|
||||
FixNPHAsphere(class LAMMPS *, int, char **);
|
||||
~FixNPHAsphere() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,7 +27,6 @@ namespace LAMMPS_NS {
|
||||
class FixNPTAsphere : public FixNHAsphere {
|
||||
public:
|
||||
FixNPTAsphere(class LAMMPS *, int, char **);
|
||||
~FixNPTAsphere() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,9 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNVEAsphere : public FixNVE {
|
||||
public:
|
||||
FixNVEAsphere(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
|
||||
@ -27,8 +27,8 @@ namespace LAMMPS_NS {
|
||||
class FixNVEAsphereNoforce : public FixNVENoforce {
|
||||
public:
|
||||
FixNVEAsphereNoforce(class LAMMPS *, int, char **);
|
||||
void initial_integrate(int);
|
||||
void init();
|
||||
void initial_integrate(int) override;
|
||||
void init() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
|
||||
@ -27,11 +27,10 @@ namespace LAMMPS_NS {
|
||||
class FixNVELine : public FixNVE {
|
||||
public:
|
||||
FixNVELine(class LAMMPS *, int, char **);
|
||||
~FixNVELine() {}
|
||||
int setmask();
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double MINUSPI, TWOPI;
|
||||
|
||||
@ -27,11 +27,10 @@ namespace LAMMPS_NS {
|
||||
class FixNVETri : public FixNVE {
|
||||
public:
|
||||
FixNVETri(class LAMMPS *, int, char **);
|
||||
~FixNVETri() {}
|
||||
int setmask();
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
|
||||
@ -27,7 +27,6 @@ namespace LAMMPS_NS {
|
||||
class FixNVTAsphere : public FixNHAsphere {
|
||||
public:
|
||||
FixNVTAsphere(class LAMMPS *, int, char **);
|
||||
~FixNVTAsphere() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -18,18 +18,18 @@
|
||||
|
||||
#include "pair_gayberne.h"
|
||||
|
||||
#include <cmath>
|
||||
#include "math_extra.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_ellipsoid.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "citeme.h"
|
||||
#include "memory.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neighbor.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
||||
@ -27,18 +27,18 @@ namespace LAMMPS_NS {
|
||||
class PairGayBerne : public Pair {
|
||||
public:
|
||||
PairGayBerne(LAMMPS *lmp);
|
||||
virtual ~PairGayBerne();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
~PairGayBerne() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
|
||||
protected:
|
||||
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class PairLineLJ : public Pair {
|
||||
public:
|
||||
PairLineLJ(class LAMMPS *);
|
||||
virtual ~PairLineLJ();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
~PairLineLJ() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
||||
@ -27,16 +27,16 @@ namespace LAMMPS_NS {
|
||||
class PairRESquared : public Pair {
|
||||
public:
|
||||
PairRESquared(LAMMPS *lmp);
|
||||
virtual ~PairRESquared();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
~PairRESquared() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
|
||||
protected:
|
||||
enum { SPHERE_SPHERE, SPHERE_ELLIPSE, ELLIPSE_SPHERE, ELLIPSE_ELLIPSE };
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class PairTriLJ : public Pair {
|
||||
public:
|
||||
PairTriLJ(class LAMMPS *);
|
||||
virtual ~PairTriLJ();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
double init_one(int, int);
|
||||
~PairTriLJ() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
||||
@ -37,91 +37,91 @@ class FixATC : public Fix {
|
||||
public:
|
||||
/** constructor & destructor */
|
||||
FixATC(class LAMMPS *, int, char **);
|
||||
~FixATC();
|
||||
~FixATC() override;
|
||||
|
||||
/** initialization functions */
|
||||
void init();
|
||||
void init_list(int id, NeighList *ptr);
|
||||
void setup(int vflag);
|
||||
void min_setup(int vflag);
|
||||
void init() override;
|
||||
void init_list(int id, NeighList *ptr) override;
|
||||
void setup(int vflag) override;
|
||||
void min_setup(int vflag) override;
|
||||
|
||||
/** setmask: tell LAMMPS which fix methods to call */
|
||||
int setmask();
|
||||
int setmask() override;
|
||||
|
||||
/** initial_integrate */
|
||||
void initial_integrate(int vflag);
|
||||
void initial_integrate(int vflag) override;
|
||||
|
||||
/** after first integrate phase */
|
||||
void post_integrate();
|
||||
void post_integrate() override;
|
||||
|
||||
/** final_integrate */
|
||||
void final_integrate();
|
||||
void final_integrate() override;
|
||||
|
||||
/** end of step for run or minimize */
|
||||
void end_of_step();
|
||||
void end_of_step() override;
|
||||
|
||||
/** pre_exchange is used to modify fix-specific data
|
||||
and is called before domain->pbc() and comm->exchange(). */
|
||||
void setup_pre_exchange();
|
||||
void pre_exchange();
|
||||
void min_pre_exchange();
|
||||
void setup_pre_exchange() override;
|
||||
void pre_exchange() override;
|
||||
void min_pre_exchange() override;
|
||||
|
||||
double memory_usage();
|
||||
void grow_arrays(int);
|
||||
void copy_arrays(int, int, int);
|
||||
double memory_usage() override;
|
||||
void grow_arrays(int) override;
|
||||
void copy_arrays(int, int, int) override;
|
||||
|
||||
/** pack_exchange called from atom_vec->pack_exchange()
|
||||
and packs fix-specific data for a given real (local)
|
||||
atom being sent to another processor. */
|
||||
int pack_exchange(int, double *);
|
||||
int pack_exchange(int, double *) override;
|
||||
|
||||
/** unpack_exchange called from atom_vec->unpack_exchange()
|
||||
and unpacks fix-specific data for a given real (local)
|
||||
atom received from another processor. */
|
||||
int unpack_exchange(int, double *);
|
||||
int unpack_exchange(int, double *) override;
|
||||
|
||||
/** pack_comm called from comm->forward_comm_fix and
|
||||
packs fix-specific data for a given ghost atom
|
||||
from exchange with another proc */
|
||||
int pack_forward_comm(int, int *, double *, int, int *);
|
||||
int pack_forward_comm(int, int *, double *, int, int *) override;
|
||||
|
||||
/** unpack_comm called from comm->forward_comm_fix and
|
||||
unpacks fix-specific data for a given ghost atom
|
||||
from exchange with another proc */
|
||||
void unpack_forward_comm(int, int, double *);
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
|
||||
/** pre_neighbor is used to modify fix-specific data
|
||||
and is called before neighbor list is built in
|
||||
neighbor->build(). */
|
||||
void pre_neighbor();
|
||||
void setup_pre_neighbor();
|
||||
void pre_neighbor() override;
|
||||
void setup_pre_neighbor() override;
|
||||
|
||||
/** pre/post_force is used to modify fix-specific data
|
||||
and is before/after the various force computations. */
|
||||
void pre_force(int vflag);
|
||||
void post_force(int vflag);
|
||||
void pre_force(int vflag) override;
|
||||
void post_force(int vflag) override;
|
||||
|
||||
/** post_run is called after a run completes */
|
||||
void post_run();
|
||||
void post_run() override;
|
||||
|
||||
/** min_pre_force is called before forces are calculated in minimize */
|
||||
void min_pre_force(int vflag);
|
||||
void min_pre_force(int vflag) override;
|
||||
|
||||
/** min_post_force is called after forces are calculated in minimize */
|
||||
void min_post_force(int vflag);
|
||||
void min_post_force(int vflag) override;
|
||||
|
||||
/** modify atc parameters (parser) */
|
||||
int modify_param(int narg, char **arg);
|
||||
int modify_param(int narg, char **arg) override;
|
||||
|
||||
/** calls ATC_Method to handle restarting/checkpointing */
|
||||
/** these four methods are for writing per-atom quantities */
|
||||
int pack_restart(int, double *);
|
||||
void unpack_restart(int, int);
|
||||
int size_restart(int);
|
||||
int maxsize_restart();
|
||||
int pack_restart(int, double *) override;
|
||||
void unpack_restart(int, int) override;
|
||||
int size_restart(int) override;
|
||||
int maxsize_restart() override;
|
||||
/** these two methods are for writing all other quantities */
|
||||
void write_restart(FILE *);
|
||||
void restart(char *);
|
||||
void write_restart(FILE *) override;
|
||||
void restart(char *) override;
|
||||
|
||||
/** accessor function for ATC_Method class pointer */
|
||||
const ATC::ATC_Method *atc() { return atc_; }
|
||||
@ -130,9 +130,9 @@ class FixATC : public Fix {
|
||||
LAMMPS *lammps_;
|
||||
|
||||
/** functions for "thermo" output */
|
||||
virtual double compute_scalar();
|
||||
virtual double compute_vector(int n);
|
||||
virtual double compute_array(int irow, int icol);
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int n) override;
|
||||
double compute_array(int irow, int icol) override;
|
||||
double dtv, dtf;
|
||||
ATC::ATC_Method *atc_;
|
||||
};
|
||||
|
||||
@ -28,12 +28,12 @@ class AtomVecWavepacket : public AtomVec {
|
||||
public:
|
||||
AtomVecWavepacket(class LAMMPS *);
|
||||
|
||||
void grow_pointers();
|
||||
void force_clear(int, size_t);
|
||||
void create_atom_post(int);
|
||||
void data_atom_post(int);
|
||||
int property_atom(char *);
|
||||
void pack_property_atom(int, double *, int, int);
|
||||
void grow_pointers() override;
|
||||
void force_clear(int, size_t) override;
|
||||
void create_atom_post(int) override;
|
||||
void data_atom_post(int) override;
|
||||
int property_atom(char *) override;
|
||||
void pack_property_atom(int, double *, int, int) override;
|
||||
|
||||
private:
|
||||
int *spin;
|
||||
|
||||
@ -31,13 +31,13 @@ namespace LAMMPS_NS {
|
||||
class FixNVEAwpmd : public Fix {
|
||||
public:
|
||||
FixNVEAwpmd(class LAMMPS *, int, char **);
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void initial_integrate_respa(int, int, int);
|
||||
void final_integrate_respa(int, int);
|
||||
void reset_dt();
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
void initial_integrate_respa(int, int, int) override;
|
||||
void final_integrate_respa(int, int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
protected:
|
||||
double dtv, dtf;
|
||||
|
||||
@ -34,22 +34,22 @@ class PairAWPMDCut : public Pair {
|
||||
|
||||
public:
|
||||
PairAWPMDCut(class LAMMPS *);
|
||||
virtual ~PairAWPMDCut();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
~PairAWPMDCut() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
void min_pointers(double **, double **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
|
||||
void min_xf_pointers(int, double **, double **);
|
||||
void min_xf_get(int);
|
||||
void min_x_set(int);
|
||||
double memory_usage();
|
||||
void min_xf_pointers(int, double **, double **) override;
|
||||
void min_xf_get(int) override;
|
||||
void min_x_set(int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
int flexible_pressure_flag;
|
||||
|
||||
@ -38,11 +38,11 @@ const int NUM_CUBIC_SPLINE_COLUMNS = 5; // cubic spline columns passed to co
|
||||
class ComputePressureBocs : public Compute {
|
||||
public:
|
||||
ComputePressureBocs(class LAMMPS *, int, char **);
|
||||
virtual ~ComputePressureBocs();
|
||||
virtual void init();
|
||||
virtual double compute_scalar();
|
||||
virtual void compute_vector();
|
||||
void reset_extra_compute_fix(const char *);
|
||||
~ComputePressureBocs() override;
|
||||
void init() override;
|
||||
double compute_scalar() override;
|
||||
void compute_vector() override;
|
||||
void reset_extra_compute_fix(const char *) override;
|
||||
|
||||
double compute_cg_scalar();
|
||||
double get_cg_p_corr(int, double *, int, double, double);
|
||||
|
||||
@ -30,26 +30,26 @@ namespace LAMMPS_NS {
|
||||
class FixBocs : public Fix {
|
||||
public:
|
||||
FixBocs(class LAMMPS *, int, char **); // MRD NJD
|
||||
virtual ~FixBocs(); // MRD NJD
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void setup(int);
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void initial_integrate_respa(int, int, int);
|
||||
void pre_force_respa(int, int, int);
|
||||
void final_integrate_respa(int, int);
|
||||
virtual void pre_exchange();
|
||||
double compute_scalar();
|
||||
virtual double compute_vector(int);
|
||||
void write_restart(FILE *);
|
||||
~FixBocs() override; // MRD NJD
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void setup(int) override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
void initial_integrate_respa(int, int, int) override;
|
||||
void pre_force_respa(int, int, int) override;
|
||||
void final_integrate_respa(int, int) override;
|
||||
void pre_exchange() override;
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int) override;
|
||||
void write_restart(FILE *) override;
|
||||
virtual int pack_restart_data(double *); // pack restart data
|
||||
virtual void restart(char *);
|
||||
int modify_param(int, char **);
|
||||
void reset_target(double);
|
||||
void reset_dt();
|
||||
virtual void *extract(const char *, int &);
|
||||
double memory_usage();
|
||||
void restart(char *) override;
|
||||
int modify_param(int, char **) override;
|
||||
void reset_target(double) override;
|
||||
void reset_dt() override;
|
||||
void *extract(const char *, int &) override;
|
||||
double memory_usage() override;
|
||||
|
||||
protected:
|
||||
int dimension, which;
|
||||
|
||||
@ -28,21 +28,21 @@ namespace LAMMPS_NS {
|
||||
class BodyNparticle : public Body {
|
||||
public:
|
||||
BodyNparticle(class LAMMPS *, int, char **);
|
||||
~BodyNparticle();
|
||||
~BodyNparticle() override;
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
int pack_data_body(tagint, int, double *);
|
||||
int write_data_body(FILE *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
void data_body(int, int, int, int *, double *) override;
|
||||
int pack_data_body(tagint, int, double *) override;
|
||||
int write_data_body(FILE *, double *) override;
|
||||
double radius_body(int, int, int *, double *) override;
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
int noutrow(int) override;
|
||||
int noutcol() override;
|
||||
void output(int, int, double *) override;
|
||||
int image(int, double, double, int *&, double **&) override;
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
|
||||
@ -28,7 +28,7 @@ namespace LAMMPS_NS {
|
||||
class BodyRoundedPolygon : public Body {
|
||||
public:
|
||||
BodyRoundedPolygon(class LAMMPS *, int, char **);
|
||||
~BodyRoundedPolygon();
|
||||
~BodyRoundedPolygon() override;
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
int nedges(struct AtomVecBody::Bonus *);
|
||||
@ -36,17 +36,17 @@ class BodyRoundedPolygon : public Body {
|
||||
double enclosing_radius(struct AtomVecBody::Bonus *);
|
||||
double rounded_radius(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
int pack_data_body(tagint, int, double *);
|
||||
int write_data_body(FILE *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
void data_body(int, int, int, int *, double *) override;
|
||||
int pack_data_body(tagint, int, double *) override;
|
||||
int write_data_body(FILE *, double *) override;
|
||||
double radius_body(int, int, int *, double *) override;
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
int noutrow(int) override;
|
||||
int noutcol() override;
|
||||
void output(int, int, double *) override;
|
||||
int image(int, double, double, int *&, double **&) override;
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
|
||||
@ -28,7 +28,7 @@ namespace LAMMPS_NS {
|
||||
class BodyRoundedPolyhedron : public Body {
|
||||
public:
|
||||
BodyRoundedPolyhedron(class LAMMPS *, int, char **);
|
||||
~BodyRoundedPolyhedron();
|
||||
~BodyRoundedPolyhedron() override;
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
int nedges(struct AtomVecBody::Bonus *);
|
||||
@ -38,17 +38,17 @@ class BodyRoundedPolyhedron : public Body {
|
||||
double enclosing_radius(struct AtomVecBody::Bonus *);
|
||||
double rounded_radius(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
int pack_data_body(tagint, int, double *);
|
||||
int write_data_body(FILE *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *) override;
|
||||
void data_body(int, int, int, int *, double *) override;
|
||||
int pack_data_body(tagint, int, double *) override;
|
||||
int write_data_body(FILE *, double *) override;
|
||||
double radius_body(int, int, int *, double *) override;
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
int noutrow(int) override;
|
||||
int noutcol() override;
|
||||
void output(int, int, double *) override;
|
||||
int image(int, double, double, int *&, double **&) override;
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
|
||||
@ -27,10 +27,10 @@ namespace LAMMPS_NS {
|
||||
class ComputeBodyLocal : public Compute {
|
||||
public:
|
||||
ComputeBodyLocal(class LAMMPS *, int, char **);
|
||||
~ComputeBodyLocal();
|
||||
void init();
|
||||
void compute_local();
|
||||
double memory_usage();
|
||||
~ComputeBodyLocal() override;
|
||||
void init() override;
|
||||
void compute_local() override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
int nvalues;
|
||||
|
||||
@ -27,14 +27,14 @@ namespace LAMMPS_NS {
|
||||
class ComputeTempBody : public Compute {
|
||||
public:
|
||||
ComputeTempBody(class LAMMPS *, int, char **);
|
||||
~ComputeTempBody();
|
||||
void init();
|
||||
void setup();
|
||||
double compute_scalar();
|
||||
void compute_vector();
|
||||
~ComputeTempBody() override;
|
||||
void init() override;
|
||||
void setup() override;
|
||||
double compute_scalar() override;
|
||||
void compute_vector() override;
|
||||
|
||||
void remove_bias(int, double *);
|
||||
void restore_bias(int, double *);
|
||||
void remove_bias(int, double *) override;
|
||||
void restore_bias(int, double *) override;
|
||||
|
||||
private:
|
||||
int mode;
|
||||
|
||||
@ -21,16 +21,15 @@ namespace LAMMPS_NS {
|
||||
class FixNHBody : public FixNH {
|
||||
public:
|
||||
FixNHBody(class LAMMPS *, int, char **);
|
||||
virtual ~FixNHBody() {}
|
||||
void init();
|
||||
void init() override;
|
||||
|
||||
protected:
|
||||
double dtq;
|
||||
class AtomVecBody *avec;
|
||||
|
||||
void nve_v();
|
||||
void nve_x();
|
||||
void nh_v_temp();
|
||||
void nve_v() override;
|
||||
void nve_x() override;
|
||||
void nh_v_temp() override;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,7 +27,6 @@ namespace LAMMPS_NS {
|
||||
class FixNPHBody : public FixNHBody {
|
||||
public:
|
||||
FixNPHBody(class LAMMPS *, int, char **);
|
||||
~FixNPHBody() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,7 +27,6 @@ namespace LAMMPS_NS {
|
||||
class FixNPTBody : public FixNHBody {
|
||||
public:
|
||||
FixNPTBody(class LAMMPS *, int, char **);
|
||||
~FixNPTBody() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,9 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNVEBody : public FixNVE {
|
||||
public:
|
||||
FixNVEBody(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dtq;
|
||||
|
||||
@ -27,7 +27,6 @@ namespace LAMMPS_NS {
|
||||
class FixNVTBody : public FixNHBody {
|
||||
public:
|
||||
FixNVTBody(class LAMMPS *, int, char **);
|
||||
~FixNVTBody() {}
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class FixWallBodyPolygon : public Fix {
|
||||
public:
|
||||
FixWallBodyPolygon(class LAMMPS *, int, char **);
|
||||
virtual ~FixWallBodyPolygon();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
void reset_dt();
|
||||
~FixWallBodyPolygon() override;
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void setup(int) override;
|
||||
void post_force(int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class FixWallBodyPolyhedron : public Fix {
|
||||
public:
|
||||
FixWallBodyPolyhedron(class LAMMPS *, int, char **);
|
||||
virtual ~FixWallBodyPolyhedron();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
void reset_dt();
|
||||
~FixWallBodyPolyhedron() override;
|
||||
int setmask() override;
|
||||
void init() override;
|
||||
void setup(int) override;
|
||||
void post_force(int) override;
|
||||
void reset_dt() override;
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class PairBodyNparticle : public Pair {
|
||||
public:
|
||||
PairBodyNparticle(class LAMMPS *);
|
||||
~PairBodyNparticle();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
~PairBodyNparticle() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class PairBodyRoundedPolygon : public Pair {
|
||||
public:
|
||||
PairBodyRoundedPolygon(class LAMMPS *);
|
||||
~PairBodyRoundedPolygon();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
~PairBodyRoundedPolygon() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
|
||||
@ -27,12 +27,12 @@ namespace LAMMPS_NS {
|
||||
class PairBodyRoundedPolyhedron : public Pair {
|
||||
public:
|
||||
PairBodyRoundedPolyhedron(class LAMMPS *);
|
||||
~PairBodyRoundedPolyhedron();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
~PairBodyRoundedPolyhedron() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double init_one(int, int) override;
|
||||
|
||||
virtual void kernel_force(double R, int itype, int jtype, double &energy, double &fpair);
|
||||
|
||||
|
||||
@ -27,9 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixBrownian : public FixBrownianBase {
|
||||
public:
|
||||
FixBrownian(class LAMMPS *, int, char **);
|
||||
virtual ~FixBrownian(){};
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
|
||||
private:
|
||||
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void initial_integrate_templated();
|
||||
|
||||
@ -27,9 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixBrownianAsphere : public FixBrownianBase {
|
||||
public:
|
||||
FixBrownianAsphere(class LAMMPS *, int, char **);
|
||||
virtual ~FixBrownianAsphere(){};
|
||||
void initial_integrate(int);
|
||||
void init();
|
||||
|
||||
void initial_integrate(int) override;
|
||||
void init() override;
|
||||
|
||||
protected:
|
||||
class AtomVecEllipsoid *avec;
|
||||
|
||||
@ -21,10 +21,10 @@ namespace LAMMPS_NS {
|
||||
class FixBrownianBase : public Fix {
|
||||
public:
|
||||
FixBrownianBase(class LAMMPS *, int, char **);
|
||||
virtual ~FixBrownianBase();
|
||||
void init();
|
||||
int setmask();
|
||||
void reset_dt();
|
||||
~FixBrownianBase() override;
|
||||
void init() override;
|
||||
int setmask() override;
|
||||
void reset_dt() override;
|
||||
|
||||
protected:
|
||||
int seed; // RNG seed
|
||||
|
||||
@ -27,9 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixBrownianSphere : public FixBrownianBase {
|
||||
public:
|
||||
FixBrownianSphere(class LAMMPS *, int, char **);
|
||||
virtual ~FixBrownianSphere(){};
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
|
||||
private:
|
||||
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void initial_integrate_templated();
|
||||
|
||||
@ -26,11 +26,11 @@ namespace LAMMPS_NS {
|
||||
class FixPropelSelf : public Fix {
|
||||
public:
|
||||
FixPropelSelf(class LAMMPS *, int, char **);
|
||||
virtual ~FixPropelSelf(){};
|
||||
void init();
|
||||
void post_force(int);
|
||||
void setup(int);
|
||||
int setmask();
|
||||
|
||||
void init() override;
|
||||
void post_force(int) override;
|
||||
void setup(int) override;
|
||||
int setmask() override;
|
||||
|
||||
private:
|
||||
double magnitude;
|
||||
|
||||
@ -27,11 +27,10 @@ namespace LAMMPS_NS {
|
||||
class AtomVecOxdna : public AtomVec {
|
||||
public:
|
||||
AtomVecOxdna(class LAMMPS *);
|
||||
~AtomVecOxdna() = default;
|
||||
|
||||
void grow_pointers();
|
||||
void data_atom_post(int);
|
||||
void data_bonds_post(int, int, tagint, tagint, tagint);
|
||||
void grow_pointers() override;
|
||||
void data_atom_post(int) override;
|
||||
void data_bonds_post(int, int, tagint, tagint, tagint) override;
|
||||
|
||||
private:
|
||||
tagint *id5p;
|
||||
|
||||
@ -27,8 +27,7 @@ namespace LAMMPS_NS {
|
||||
class BondOxdna2Fene : public BondOxdnaFene {
|
||||
public:
|
||||
BondOxdna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
|
||||
virtual ~BondOxdna2Fene() {}
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
|
||||
void compute_interaction_sites(double *, double *, double *, double *) const override;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,16 +27,16 @@ namespace LAMMPS_NS {
|
||||
class BondOxdnaFene : public Bond {
|
||||
public:
|
||||
BondOxdnaFene(class LAMMPS *lmp) : Bond(lmp) {}
|
||||
virtual ~BondOxdnaFene();
|
||||
~BondOxdnaFene() override;
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
|
||||
virtual void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double equilibrium_distance(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_data(FILE *);
|
||||
double single(int, double, int, int, double &);
|
||||
void compute(int, int) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_style() override;
|
||||
double equilibrium_distance(int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
double single(int, double, int, int, double &) override;
|
||||
|
||||
protected:
|
||||
double *k, *Delta, *r0; // FENE
|
||||
|
||||
@ -27,9 +27,8 @@ namespace LAMMPS_NS {
|
||||
class BondOxrna2Fene : public BondOxdnaFene {
|
||||
public:
|
||||
BondOxrna2Fene(class LAMMPS *lmp) : BondOxdnaFene(lmp) {}
|
||||
virtual ~BondOxrna2Fene() {}
|
||||
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *) const;
|
||||
void compute_interaction_sites(double *, double *, double *, double *) const override;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -27,9 +27,9 @@ namespace LAMMPS_NS {
|
||||
class FixNVEDot : public FixNVE {
|
||||
public:
|
||||
FixNVEDot(class LAMMPS *, int, char **);
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dt, dthlf, dthlfm;
|
||||
|
||||
@ -27,10 +27,10 @@ namespace LAMMPS_NS {
|
||||
class FixNVEDotcLangevin : public FixNVE {
|
||||
public:
|
||||
FixNVEDotcLangevin(class LAMMPS *, int, char **);
|
||||
virtual ~FixNVEDotcLangevin();
|
||||
void init();
|
||||
void initial_integrate(int);
|
||||
void final_integrate();
|
||||
~FixNVEDotcLangevin() override;
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
private:
|
||||
double dt, dthlf, dthlfm, dtqrt;
|
||||
|
||||
@ -27,19 +27,19 @@ namespace LAMMPS_NS {
|
||||
class PairOxdna2Coaxstk : public Pair {
|
||||
public:
|
||||
PairOxdna2Coaxstk(class LAMMPS *);
|
||||
virtual ~PairOxdna2Coaxstk();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
void *extract(const char *, int &);
|
||||
~PairOxdna2Coaxstk() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
// coaxial stacking interaction
|
||||
|
||||
@ -27,20 +27,20 @@ namespace LAMMPS_NS {
|
||||
class PairOxdna2Dh : public Pair {
|
||||
public:
|
||||
PairOxdna2Dh(class LAMMPS *);
|
||||
virtual ~PairOxdna2Dh();
|
||||
~PairOxdna2Dh() override;
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *);
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
void *extract(const char *, int &);
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
double **qeff_dh_pf, **kappa_dh;
|
||||
|
||||
@ -27,8 +27,8 @@ namespace LAMMPS_NS {
|
||||
class PairOxdna2Excv : public PairOxdnaExcv {
|
||||
public:
|
||||
PairOxdna2Excv(class LAMMPS *lmp) : PairOxdnaExcv(lmp) {}
|
||||
virtual ~PairOxdna2Excv() {}
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
|
||||
|
||||
void compute_interaction_sites(double *, double *, double *, double *, double *) override;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -28,19 +28,19 @@ namespace LAMMPS_NS {
|
||||
class PairOxdnaCoaxstk : public Pair {
|
||||
public:
|
||||
PairOxdnaCoaxstk(class LAMMPS *);
|
||||
virtual ~PairOxdnaCoaxstk();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
void *extract(const char *, int &);
|
||||
~PairOxdnaCoaxstk() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
// coaxial stacking interaction
|
||||
|
||||
@ -27,20 +27,20 @@ namespace LAMMPS_NS {
|
||||
class PairOxdnaExcv : public Pair {
|
||||
public:
|
||||
PairOxdnaExcv(class LAMMPS *);
|
||||
virtual ~PairOxdnaExcv();
|
||||
~PairOxdnaExcv() override;
|
||||
virtual void compute_interaction_sites(double *, double *, double *, double *, double *);
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
void *extract(const char *, int &);
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
// s=sugar-phosphate backbone site, b=base site, st=stacking site
|
||||
|
||||
@ -28,19 +28,19 @@ namespace LAMMPS_NS {
|
||||
class PairOxdnaHbond : public Pair {
|
||||
public:
|
||||
PairOxdnaHbond(class LAMMPS *);
|
||||
virtual ~PairOxdnaHbond();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
void *extract(const char *, int &);
|
||||
~PairOxdnaHbond() override;
|
||||
void compute(int, int) override;
|
||||
void settings(int, char **) override;
|
||||
void coeff(int, char **) override;
|
||||
void init_list(int, class NeighList *) override;
|
||||
double init_one(int, int) override;
|
||||
void write_restart(FILE *) override;
|
||||
void read_restart(FILE *) override;
|
||||
void write_restart_settings(FILE *) override;
|
||||
void read_restart_settings(FILE *) override;
|
||||
void write_data(FILE *) override;
|
||||
void write_data_all(FILE *) override;
|
||||
void *extract(const char *, int &) override;
|
||||
|
||||
protected:
|
||||
// h-bonding interaction
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user